Saturday, March 31, 2012

Japan: Quake/Tsunami Risks Greater Than Previously Thought



Credit Wikipedia

# 6255


We’ve two seismic studies announced today in Japan - one regarding Tokyo’s vulnerability to a major earthquake and the other on the tsunami risk that would result from an offshore earthquake in the Nankai Trough.


Both substantially escalate the amount of damage that could be expected over previous estimates.


First stop, the Nankai quake scenario, as reported by the Japan Times.



20-meter tsunami projected from Honshu to Kyushu

Nankai quake scenario menaces Pacific coast


Wide swaths of the Pacific coastline stretching from Honshu to Kyushu may be hit by tsunami over 20 meters high if a newly feared megaquake occurs in the Nankai Trough, a Cabinet Office panel warned Saturday.

(Continue . . . )



Kuroshio, Kochi Prefecture could see a tsunami up to 34.4 meters (112 feet, or as high as a 10 story building), while parts of Shizuoka, Kochi and Miyazaki prefectures could see tidal waves of 10 to 20 meters.


Such an earthquake could send tsunami waves towards other Pacific shorelines, as well.


The second announcement comes from Japan’s Ministry of Education, Culture, Sports, Science and Technology (MEXT) which has determined that the fault line lying under Tokyo is shallower than previously thought, and capable of producing more damage than had been earlier estimated.

This report from Reuters:


Major quake impact on Tokyo could be worse than thought-study

31 Mar 2012 09:10

Source: reuters // Reuters

TOKYO, March 31 (Reuters) - The impact on Tokyo from a major quake could be much more devastating than the government has predicted, a new study shows.


The study by the Ministry of Education, Culture, Sports, Science and Technology comes just over a year after one of the biggest tremors on record struck Japan'se northeast coast, triggering a massive tsunami and the world's worst nuclear crisis in 25 years.

(Continue . . .)



You may recall that a couple of months ago (see Academics Debate Odds Of Tokyo Earthquake) we saw a report indicating that some scientists believe that the odds of a major earthquake striking Tokyo (previously estimated at 70% within 30 years) are overly optimistic, and that there is a 70% chance of a major Tokyo quake in the next four years.


And last year, in Divining Japan’s Seismic Future, I wrote about the most widely anticipated seismic event for Japan - the Tokai Earthquake – expected to be an 8+ magnitude, and forecast to occur between the Bay of Suruga and Cape Omasezaki in Shizuoka Prefecture sometime in the near future.




Major earthquakes have occurred in this region every 100-150 years, with the most recent recorded in 1498, 1605, 1707 and 1854.


That puts the Tokai region 157 years since their last major quake, and in the estimation of Dr Kiyoo Mogi – Japan’s leading seismologist – well overdue for another.   In 1969, Dr Mogi began warning that the Tokai area was particularly vulnerable, and today the area is monitored continually by the JMA.


Which is why the Prime Minister of Japan called upon Chubu Electric to shut down its No. 4 and No. 5 reactors at the Hamaoka nuclear plant last May, located roughly 200 km south-west of Tokyo.


While all of this is of greatest concern to those living in Japan, a major earthquake in one of the great cities of the world would not only be a horrendous human tragedy, it could cause economic repercussions around the globe.


In two blogs from last year we looked at the possible ripple effects of `Global Shocks’.


Last December in DFID: World Unprepared For Future Shocks  the UK’s DFID (Department for International Development) warned that with global economies in turmoil, and recessionary fears continuing to spread, finding money for many relief, humanitarian, or other worthwhile projects becomes more difficult.


And last July, in (OECD Report: Future Global Shocks), where we looked at a 139 page report  released by the OECD (The Organisation for Economic Co-operation and Development) that warned - as the world becomes more interconnected and interdependent - that `Global Shocks’ to the world economy become more likely.


In the report, they define a Global Shock as: a rapid onset event with severely disruptive consequences covering at least two continents.


They write:

Extremely disruptive events, such as earthquakes, volcanoes, financial crises and political revolutions destabilize critical systems of supply, producing economic spillovers that reach far beyond
their geographical point of origin.


While such extreme events have been relatively rare in the past, they seem poised to occur with greater frequency in the future. Global interconnections accompanying economic integration enable some risks to propagate rapidly around the world.



The bottom line here is that the world is now so interconnected – that while most disasters are localized - their economic and societal impacts can be felt thousands of miles away and can persist for months.


Of course Japan doesn’t have the market cornered when it comes to disasters; the United States, Europe, and the rest of the world are all capable of producing equally disruptive global shocks.  


Ultimately, a nation’s resilience in the face of a major crisis –whether it be local or global - comes from the bottom up, not from the top down.


Which is why agencies, like the ones below, urge greater individual, family, and community preparedness.






A few of my preparedness blogs from the past include:


When 72 Hours Isn’t Enough

Planning To Survive

An Appropriate Level Of Preparedness

In An Emergency, Who Has Your Back?

The Gift Of Preparedness: 2011

Friday, March 30, 2012

NSABB Clears H5N1 Studies For Publication


# 6254



From Helen Branswell this evening, a report that the NSABB – after reviewing new data submitted by flu researcher Ron Fouchier – has cleared the way for the publication of both his, and Yoshihiro Kawaoka’s work on ferret transmissible H5N1.


The vote to publish Karaoka’s paper was unanimous, while the vote for Fourchier’s was 12 to 6.


The NSABB serves in an advisory capacity only, and it will be up to the United States government to either accept or reject their recommendations.



Follow the link below for the story by Helen Branswell.


US biosecurity panel clears publication path for controversial bird flu studies

By Helen Branswell, The Canadian Press |   


For more on what the future of U.S. government sponsored life sciences research will look like, you may wish to revisit yesterday’s blog on U.S. Issues New DURC Oversight Rules.

Study: Aerosolized Influenza And PPEs


Photo Credit PHIL (Public Health Image Library)


# 6253


We’ve a new study, appearing yesterday in the journal Clinical Infectious Diseases, that once again raises questions over the effectiveness of different types of PPEs (Personal Protective Equipment) used by Health Care Workers (HCWs) in an infectious environment.




Ideally, the well-protected HCW (Health Care Worker) working in an infectious environment would be wearing an N95 mask, gloves, gown and eye protection.


But during the opening months of the 2009 pandemic, it became apparent that our world faced a shortage of PPEs, and so strategies were adopted to maximize their use.


In some cases nurses were issued only one N95 mask to be used for an entire 8 hour shift, and told to don it only when in direct contact with a potentially infected patient.


In other venues, HCWs were issued surgical masks in lieu of N95s, despite the recommendation at the time from the CDC that N95 masks were the preferred level of protection.


Fortunately, the virulence of the novel 2009 H1N1 virus was less than originally feared. Had the pandemic carried a higher mortality and morbidity rate, the lack of PPEs would have become a much bigger issue.


For decades, the assumption was that only properly fitted N95 masks protected the wearer, and that surgical masks were only worn by HCWs to protect the patient during invasive procedures.


image image

N-95 Respirator         Surgical mask


But in recent years we’ve seen dueling studies that alternately show surgical masks to be a reasonable protective barrier against respiratory viruses  . . . or pretty much useless.


Take your pick.


A brief tour of these conflicting reports include:



In October of 2009 the NEJM published a perspective article (see NEJM Perspective: Respiratory Protection For HCWs) based on a 2009 IOM evaluation of surgical masks vs. respirators, and came out in favor of the N95.


A few days later JAMA (Journal of the American Medical Association) published a study which reported that HCWs using surgical masks experienced `noninferior rates of laboratory-confirmed influenza’.


In March of 2010, we saw the following study (see Study: Efficacy of Facemasks Vs. Respirators) in Clinical Infectious Diseases, that suggested that surgical masks are just as effective as respirators in protecting HCWs.


In guidance, updated as late as March of 2010, the CDC continued to recommend N95 respirators for HCWs who came in close contact with suspected or confirmed influenza patients.


But in June of 2010, the CDC proposed new guidance that relaxed those recommendations to using surgical masks for routine care, and reserving N95 masks for aerosol producing procedures (intubation, suctioning, etc).


Still, the controversy remains. 


Adding to the confusion, we’ve seen recent studies that give more credence to the notion that influenza may be spread in aerosolized form (see Study: Aerosolized Transmission Of Influenza), as opposed to primarily by large droplets, and may also be contracted via the transocular route.


Our knowledge of how influenza spreads, and what barriers work well to protect HCWs, remains limited.


All of which serves as prelude to this new study, that simulates the aerosolization of influenza viruses and measured the protective qualities of surgical masks and respirators by constructing a simulated  exam room using `coughing and breathing manikins’.


Although the full paper is behind a pay wall, we can get a pretty good idea of the study’s content from the abstract.


Detection of Infectious Influenza Virus in Cough Aerosols Generated in a Simulated Patient Examination Room

John D. Noti, William G. Lindsley, Francoise M. Blachere, Gang Cao, Michael L. Kashon, Robert E. Thewlis, Cynthia M. McMillen, William P. King, Jonathan V. Szalajda, and Donald H. Beezhold

ABSTRACT (Excerpts)

Methods. National Institute for Occupational Safety and Health aerosol samplers collected size-fractionated aerosols for 60 minutes at the mouth of the breathing manikin, beside the mouth, and at 3 other locations in the room. Total recovered virus was quantitated by quantitative polymerase chain reaction and infectivity was determined by the viral plaque assay and an enhanced infectivity assay.

Results. Infectious influenza was recovered in all aerosol fractions (5.0% in >4 μm aerodynamic diameter, 75.5% in 1–4 μm, and 19.5% in <1 μm; n = 5). Tightly sealing a mask to the face blocked entry of 94.5% of total virus and 94.8% of infectious virus (n = 3). A tightly sealed respirator blocked 99.8% of total virus and 99.6% of infectious virus (n = 3). A poorly fitted respirator blocked 64.5% of total virus and 66.5% of infectious virus (n = 3). A mask documented to be loosely fitting by a PortaCount fit tester, to simulate how masks are worn by healthcare workers, blocked entry of 68.5% of total virus and 56.6% of infectious virus (n = 2).

Conclusions. These results support a role for aerosol transmission and represent the first reported laboratory study of the efficacy of masks and respirators in blocking inhalation of influenza in aerosols. The results indicate that a poorly fitted respirator performs no better than a loosely fitting mask.


The results here are fascinating.


First, this study provides more evidence of the role of aerosolized virus particles in the transmission of influenza. Important because these particles can stay aloft and viable for some time, and spread further than large droplets can.


From a more practical standpoint, the big revelation is that a surgical mask, as normally worn by HCWs, only blocked 56.6% of infectious virus particles.


But . . . if you tightly seal the surgical mask against the face , you can achieve a level of protection approaching that of a well fitted N95 respirator (94.8% versus 99.6%).


And a poorly fitted N-95 respirator provided little more protection (66.5%) than a loosely fitted surgical mask.


This study will no doubt add further fuel to the debate over what constitutes appropriate PPEs for healthcare workers during a pandemic.


For the rest of us, the takeaway message here is that surgical masks (which are much cheaper, and easier to stockpile) appear to provide a reasonable level of protection against aerosolized influenza viruses when tightly sealed against the face.


Which means, I suppose, that now I need to think about beefing up my supply of paper surgical tape.

Thursday, March 29, 2012

U.S. Issues New DURC Oversight Rules


BSL-4 Lab Worker - Photo Credit –USAMRIID


# 6252



While the current H5N1 research row has centered around the publication of two specific research projects (see NSABB To Re-examine H5N1 Research Risks), the bigger issues at play involve how we oversee (and fund) future life sciences research in order to avoid future controversies.


To that end, today the Office of Science Policy at the NIH released a 4 page set of guidelines for DURC (Duel Use Research of Concern) projects, and ordered a review of all current life sciences projects.


For those unfamiliar with the lexicon of biomedical research, DURC in this new policy is defined as:


. . . life sciences research that, based on current understanding, can be reasonably anticipated to provide knowledge, information, products, or technologies that could be directly misapplied to pose a significant threat with broad potential consequences to public health and safety, agricultural crops and other plants, animals, the environment, materiel, or national security


The scope of this new policy is to cover research on the most dangerous of biological organisms, listing;


a)  Avian influenza virus (highly pathogenic) 
b)  Bacillus anthracis
c)  Botulinum neurotoxin
d)  Burkholderia mallei
e)  Burkholderia pseudomallei
f)  Ebola virus
g)  Foot-and-mouth disease virus
h)  Francisella tularensis
i)  Marburg virus

j)  Reconstructed 1918 Influenza virus

k)  Rinderpest virus
l)  Toxin-producing strains of Clostridium botulinum
m) Variola major virus
n)  Variola minor virus
o)  Yersinia pestis

Specifically any research that seeks to:


a)  Enhances the harmful consequences of the agent or toxin; 

b)  Disrupts immunity or the effectiveness of an immunization against the agent or toxin without
clinical or agricultural justification;

c)  Confers to the  agent or toxin resistance to clinically or agriculturally useful prophylactic or
therapeutic interventions against that agent or toxin or facilitates their ability to evade detection methodologies;

d)  Increases the stability, transmissibility, or the ability to disseminate the agent or toxin; 

e)  Alters the host range or tropism of the agent or toxin;  

f)  Enhances the susceptibility of a host population to the agent or toxin; or

g)  Generates or reconstitutes an eradicated or extinct agent or toxin listed in Section (III.1) above.



While this new policy does not automatically halt or defund research found to meet the DURC definition, it does require greater agency oversight and an assessment of the risks and benefits of any research, along with the development of appropriate risk and safety measures.


As far as `teeth’ in this new policy, if perceived risks cannot be satisfactorily mitigated Federal Agencies may request voluntary redaction of scientific papers, may move to `classify’ the research, or may withhold or terminate financial support.


Agencies that conduct or fund life sciences research are instructed to perform a review to identify any projects that meet the DURC definition, and if found, to:



c)  Assess the risks and benefits of such projects, including how research methodologies may
generate risks and/or whether open access to the knowledge, information, products, or technologies  generates risk.

d)  Based on the risk assessment, in collaboration with the institution or researcher, develop a risk
mitigation plan
to apply any necessary and appropriate risk mitigation measures.  In addition:

  • i)  For DURC that is proposed and not yet funded, departments and agencies will assess
    whether to incorporate risk mitigation measures in the grant, contract, or agreement.

  • ii)  For currently funded DURC, funding departments and agencies will consider modifying the grant, contract, or agreement to incorporate risk mitigation measures. If such modifications are not possible or desirable, departments and agencies will seek voluntary implementation of mitigation measures by the institution. 



You can access the full policy on the Office of Biotechnology Activity’s News Page:


Now Available:

US Government Issues Policy on Oversight of Life Science Dual Use Resarch of Concern:

The purpose of this Policy is to establish regular review of United States Government funded or conducted research with certain high-consequence pathogens and toxins for its potential to be dual use research of concern (DURC) in order to: (a) mitigate risks where appropriate; and (b) collect information needed to inform the development of an updated policy, as needed, for the oversight of DURC. The fundamental aim of this oversight is to preserve the benefits of life sciences research while minimizing the risk of misuse of the knowledge, information, products, or technologies provided by such research.

(March 29, 2012)



And just as I was finishing this post up, I saw that Lisa Schnirring at CIDRAP NEWS has an excellent overview of this new policy.   Read it at:


US debuts life sciences dual-use research policy

Lisa Schnirring * Staff Writer


It will be interesting to see how this new policy is received by scientists working in the life sciences field.

Fukushima Nuke Plant Remains In `Precarious State’



Photo credit IAEA

# 6251


Unless we are directly affected by them, once a disaster moves off the front pages, we tend move on as the never ending parade of newer, more immediate concerns emerge.


A year ago, the world watched in horror as Japan reeled from a monstrous earthquake/tsunami followed by a major nuclear accident.


Over time, as the recovery efforts proceeded and the nuke plants were finally deemed `stable’, the triple disaster of Fukushima has faded for most of us.


But as we learn from a report in the New York Times today, the reactor at Fukushima may be in worse shape than previously admitted, and its current stability is precarious at best.


Japan Admits Nuclear Plant Still Poses Dangers


TOKYO — The damage to the core of at least one of the meltdown-stricken reactors at Fukushima could be far worse than previously thought, raising fresh concerns over the plant’s stability and gravely complicating the post-disaster cleanup, a recent internal investigation has shown.

(Continue . . .)



Follow the link to read the entire article to learn about the specifics, including much lower water levels over the fuel rods than previously reported, and much higher levels of radiation inside the containment buildings.


But the `money quote’ comes from Kazuhiko Kudo, a professor of nuclear engineering at Kyushu University, at the end of the article who warns:


“The plant is still in a precarious state.

Unfortunately, all we can do is to keep pumping water inside the reactors, and hope we don’t have another big earthquake.”


Cleanup of these plants may take decades, and until that can be accomplished, they remain vulnerable to additional seismic shocks.

MMWR: Coxsackievirus A6 Notes From The Field

Thumbnail of Vesicular eruptions in A) hand, B) foot, and C) mouth of a 6.5-year-old boy from Turku, Finland, with coxsackievirus (CV) A6 infection. Several of his fingernails shed 2 months after the pictures were taken. D) Onychomadesis in a 10-year-old boy from Seinäjoki, Finland, 2 months after hand, foot and mouth disease with CVA6 infection. Photographs courtesy of H. Kujari (A–C) and M. Linna (D).

Vesicular eruptions in A) hand, B) foot, and C) mouth of a 6.5-year-old boy from Turku, Finland, with coxsackievirus (CV) A6 infection.  Credit - CDC EID Journal


# 6250



As a follow up to a blog I wrote in February (see HFMD: An Old Illness With A New Cause), today we’ve a field report that appears in the current MMWR on an emerging coxsackievirus (CVA6) that has recently been reported in the United States.


HFMD (Hand Foot & Mouth Disease) is a very common viral infection, usually peaking late summer or early fall, and mainly seen among children under the age of 10 (although adults may be vulnerable as well).


It is caused by several of the non-polio enteroviruses.


The two most common causes of HFMD have been the Coxsackie A16 virus, and the Enterovirus-71 (EV-71), and rarely, the Coxsackie A10 virus.


The disease in the United States is commonly caused by the Coxsackie A16 virus and is generally mild. Outbreaks are not uncommon in schools and childcare facilities.


In 2008, the CDC’s EID Journal carried a dispatch describing an outbreak of HFMD in Finland due to an unusual, and apparently emerging, viral cause; the Coxsackie A6 (CVA6) virus.


Since then, we’ve seen a growing number of reports of HFMD outbreaks around the world due to this particular coxsackievirus, but until this winter, never in the United States.


Today’s MMWR brings us details of the spread and severity of these cases.


As they note: The age ranges of patients, severity of illness, seasonality of disease, and identification of CVA6 in these cases were unusual for HFMD in the United States.


The good news is - while more severe than typical HFMD, and resulting in the hospitalization of nearly 20% of the cases - no deaths from the emerging CVA6 strain were reported.


Notes from the Field: Severe Hand, Foot, and Mouth Disease Associated with Coxsackievirus A6 — Alabama, Connecticut, California, and Nevada, November 2011–February 2012


March 30, 2012 / 61(12);213-214

Hand, foot, and mouth disease (HFMD) is a common viral illness caused by enteroviruses that predominantly affects children aged <5 years. In the United States, outbreaks of HFMD typically occur during summer and autumn months. The most common cause of HFMD in the United States has been enterovirus serotype coxsackievirus A16. Most infections are asymptomatic; persons with signs and symptoms typically have a mild febrile illness with rash on the palms of the hands and soles of the feet, and sores in the mouth. HFMD also has been associated, often weeks after initial symptom onset, with nail dystrophies (e.g., Beau's lines or nail shedding).


From November 7, 2011, to February 29, 2012, CDC received reports of 63 persons with signs and symptoms of HFMD or with fever and atypical rash in Alabama (38 cases), California (seven), Connecticut (one), and Nevada (17). HFMD is not a reportable disease in the United States; the cases were identified as unusual by health-care providers or by a department of health that contacted CDC for diagnostic assistance. Clinical specimens were collected from patients in 34 of the 63 cases. Coxsackievirus A6 (CVA6) was detected in 25 (74%) of those 34 patients by reverse transcriptase–polymerase chain reaction and partial sequencing of the VP1 gene at CDC or at the California Department of Public Health. No enteroviruses were detected in the other nine patients.


Of the 63 patients, 40 (63%) were aged <2 years, and 15 (24%) were adults aged ≥18 years; 44 (70%) of the patients had exposure to a child care facility or school, and eight (53%) of the 15 adults had contact with children in child care where cases of HFMD were reported, or provided medical care or were related to a child with HFMD. Rash and fever were more severe, and hospitalization was more common than with typical HFMD. Signs of HFMD included fever (48 patients [76%]); rash on the hands or feet, or in the mouth (42 [67%]); and rash on the arms or legs (29 [46%]), face (26 [41%]), buttocks (22 [35%]), and trunk (12 [19%]). Of 46 patients with rash variables reported, the rash typically was maculopapular; vesicles were reported in 32 (70%) patients and scabs in 30 (65%) patients. Shedding of nails occurred after initial infection in two (4%) patients. Of the 63 patients, 51 (81%) sought care from a clinician, and 12 (19%) were hospitalized. Reasons for hospitalization varied and included dehydration and/or severe pain. No deaths were reported.


The age ranges of patients, severity of illness, seasonality of disease, and identification of CVA6 in these cases were unusual for HFMD in the United States. CVA6 has been associated with more severe and extensive rash than HFMD caused by other enteroviruses (1). Since 2008, international outbreaks of CVA6 HFMD in children and adults have been described (1–4), but no outbreaks had been reported in the United States previously. Although all 25 of the CVA6 strains identified in the U.S. cases were genetically closely related (based on partial VP1 gene sequences) to CVA6 strains identified in recent international outbreaks, no epidemiologic evidence (e.g., travel history) has directly linked any of the U.S. cases to importation.


HFMD is spread from person to person by contact with saliva, respiratory secretions, fluid in vesicles, and feces. Transmission of HFMD can be reduced by maintaining good hygiene, including handwashing and disinfection of surfaces in child care settings (5). CDC continues to receive reports of CVA6-associated HFMD. Persons who suspect a severe case of HFMD should contact their health-care provider. Local or state health departments may contact CDC for assistance with enterovirus laboratory diagnosis.



For more on HFMD, including the more severe Enterovirus-71 (EV-71) version found mostly in southeast Asia, you may wish to revisit the following blogs:


Vietnam’s HFMD Outbreak
China: A Recombinant EV-71
HFMD Rising In China
China Sounds Alert Over EV-71 Virus

NSABB To Re-examine H5N1 Research Risks



# 6249



Today and tomorrow the NSABB (National Science Advisory Board for Biosecurity) will reconvene to re-examine the issues surrounding the publication of controversial H5N1 research that produced a ferret-transmissible strain of bird flu.


Last September, Ron Fouchier from the Netherlands (and almost simultaneously Professor Yoshihiro Kawaoka from Wisconsin) announced success in creating enhanced strains of the avian flu virus in the laboratory, which subsequently unleashed a firestorm of controversy.


For some background, see Katherine Harmon’s Sci-Am article , New Scientist: Five Easy Mutations, & NPR: Bio-Terrorism Concerns Over Bird Flu Research.


Over the ensuing six months we’ve seen a steady stream of opinion pieces from both sides of this debate (see H5N1 Research: A Plethora Of Positions), including side forays into the lethality of the H5N1 virus (see The Great CFR Divide).


This week we’ve seen the release of additional dueling commentaries, three of which Lisa Schnirring of CIDRAP NEWS  highlighted last night in her article:


Scientists volley ahead of more dual-use H5N1 debate

Lisa Schnirring * Staff Writer

Mar 28, 2012 (CIDRAP News) – As researchers from both sides of the debate over two controversial H5N1 studies weighed in yesterday on full publication versus a more cautionary approach, two US journals said they are developing policies to address any future such instances.

(Continue . . .)



The NSABB serves strictly in an advisory role, and any policy decisions must come from the United States government. Nonetheless, all eyes will be on the NSABB as they consider this issue.


And I can think of no one better than Helen Branswell  of the Canadian Press to preview this meeting for us:


Biosecurity panel reconvenes to reexamine controversial bird flu studies

3-28-12 6:31 PM EDT  By Helen Branswell

A bid from some quarters in the U.S. to resolve the ongoing controversy over two unpublished bird flu studies will begin to play out over the next two days as government biosecurity advisers reconvene to reconsider the issue.


The National Science Advisory Board for Biosecurity will meet Thursday and Friday in Washington, D.C., to go over revised versions of the two studies and hear about the work from their principal authors, noted flu virologists Ron Fouchier of Erasmus Medical Centre in Rotterdam, the Netherlands, and Yoshihiro Kawaoka of the University of Wisconsin-Madison.

(Continue . . . )

Wednesday, March 28, 2012

Nature: Views & Opinions On Tracking H5N1



Photo Credit – FAO

# 6248


The journal Nature has today published four short opinion pieces by well known researchers on how best to track the progress of the H5N1 virus in nature.


Follow the links below to read their rationales.


First from Dr. Guan Yi, a virologist from the University of Hong Kong and a true hero of the SARS outbreak, a recommendation to:


Monitor outbreaks in domestic ducks



Next, Dr. Richard Webby from St Jude Children's Research Hospital, urges that we:

Improve surveillance of pigs



The Director of the International Reference Laboratory for Avian Influenza and Newcastle Disease in  Legnaro, Italy - Ilaria Capua - recommends:


Restore ties lost in the Arab Spring



And Jonas Waldenström, from the School of Natural Sciences, Linnaeus University, Kalmar, Sweden says we need to:


Learn more about the role of wild birds


It probably goes without saying that all of these are important parts of the H5N1 proliferation puzzle, deserving of greater resources and attention.



Additionally,  Jeremy Farrar – from the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam calls for the tools and training for responding to diseases such as bird flu to be stationed in countries where these viruses are most likely to emerge.



H5N1 surveillance: Shift expertise to where it matters

Jeremy Farrar

Nature 483, 534–535 (29 March 2012)




And last, but certainly not least, Declan Butler weighs in on the need for better surveillance in an eye-opening analysis called:


Flu surveillance lacking


Declan Butler

28 March 2012

Nature analysis highlights need for international strategy to watch for pandemic threats.

tick . . . tick . . . tick . . .



# 6247



While not greeted as warmly as the first robin of spring - in another sign of the change of seasons - this weekend after a trek in the woods I found my first tick of spring crawling up my pants leg.


With a near absence of winter this year across much of the southeast, insects – including disease vectoring ticks and mosquitoes – appear to be getting an earlier start this spring.


As you can see by the chart below, in the nymph stage, ticks are not much larger than a spec of dirt.  Tenacious hangers on to the skin, they can be easily missed when bathing. 




And the problem isn’t limited to the deep south.


A couple of weeks ago, Maryn McKenna – reporting from the ICEID conference, wrote about concerns over the upcoming Lyme season in the Northeast:


Acorns And Mice Driving Unusual Lyme Disease Risks (ICEID 2)



And even in the UK, the HPA has issued warnings about the upcoming `tick season’.



HPA advises public to be 'tick aware' to reduce the risk of Lyme disease

27 March 2012

The Health Protection Agency (HPA) is reminding people to be ‘tick aware’ this year and take sensible precautions to reduce their risk of Lyme disease, as Tick Bite Prevention Week (26 March – 1 April) begins.


Lyme disease is a bacterial infection which is transmitted by tick bites. Ticks are tiny spider-like creatures which can be found in forests, woodland, heaths, moorland areas and in suburban parkland. Most ticks do not carry the infection but any area in which ticks are present should be regarded as potential risk areas for acquiring Lyme disease. Late spring, early summer and autumn are peak times for tick bites and coincide with people venturing into the great outdoors in the warmer weather.


There were 905 laboratory-confirmed cases of Lyme disease reported to the HPA in England and Wales in 2010. The majority of cases (741) were acquired in the UK rather than overseas, with 86 per cent of these (637) identified among residents in the south of England (the South West, South East and London).


However, not all cases of Lyme disease are confirmed by laboratory testing and, as in previous years, the overall number of Lyme disease cases in England and Wales is estimated at between 2,000 and 3,000 cases a year. Incidence of Lyme disease acquired in England and Wales remains low compared to in some other European countries or in North America.


(Continue . . .)




The CDC’s Division of Vector-Borne Diseases (DVBD)  recommends taking the following steps to prevent tick borne infections:


Preventing Tick Bites

While it is a good idea to take preventive measures against ticks year-round, be extra vigilant in warmer months (April-September) when ticks are most active.

Avoid Direct Contact with Ticks

  • Avoid wooded and bushy areas with high grass and leaf litter.
  • Walk in the center of trails.

Repel Ticks with DEET or Permethrin

  • Use repellents that contain 20% or more DEET (N, N-diethyl-m-toluamide) on the exposed skin for protection that lasts up to several hours. Always follow product instructions. Parents should apply this product to their children, avoiding hands, eyes, and mouth.
  • Use products that contain permethrin on clothing. Treat clothing and gear, such as boots, pants, socks and tents. It remains protective through several washings. Pre-treated clothing is available and remains protective for up to 70 washings.
  • Other repellents registered by the Environmental Protection Agency (EPA) may be found at

Find and Remove Ticks from Your Body

  • Bathe or shower as soon as possible after coming indoors (preferably within two hours) to wash off and more easily find ticks that are crawling on you.
  • Conduct a full-body tick check using a hand-held or full-length mirror to view all parts of your body upon return from tick-infested areas. Parents should check their children for ticks under the arms, in and around the ears, inside the belly button, behind the knees, between the legs, around the waist, and especially in their hair.
  • Examine gear and pets. Ticks can ride into the home on clothing and pets, then attach to a person later, so carefully examine pets, coats, and day packs. Tumble clothes in a dryer on high heat for an hour to kill remaining ticks.


With more than 20,000 new cases of Lyme disease reported each year, and undoubtedly many others that go unreported or undiagnosed, Lyme is one of the fastest growing emerging infectious diseases in the country.


But Lyme is not the only tick-borne illness to be aware of. Others include:



All of which illustrates the need to become more aware of the threat posed by these vicious vectors, and proactive in preventing them from passing on their diseases to you and your family.

The Tale Of The Tape




# 6247


Although it already feels like summer here in Florida, Hurricane Season is (officially) still two months away.


Every spring hurricane experts, meteorologists, public safety officials, and weather geeks assemble at the National Hurricane Conference to discuss the latest research and the upcoming hurricane season.



The conference is being held in Orlando this week, and their website describes it thusly:


Purpose of the Conference

The primary goal of the National Hurricane Conference is to improve hurricane preparedness, response, recovery and mitigation in order to save lives and property in the United States and the tropical islands of the Caribbean and Pacific. In addition, the conference serves as a national forum for federal, state and local officials to exchange ideas and recommend new policies to improve Emergency Management.

To accomplish these goals, the annual conference emphasizes:

* Lessons Learned from Hurricane Strikes.

* State of the art programs worthy of emulation.

* New ideas being tested or considered.

* Information about new or ongoing assistance programs.

* The ABC's of hurricane preparedness, response, recovery and mitigation -- in recognition of the fact that there is a continual turnover of emergency management leadership and staff.



According to an AP report yesterday (Hurricane officials: No more tape for windows By MIKE SCHNEIDER, Associated Press), one of the priorities this year is to convince the public of the folly and futility of taping their windows in advance of a hurricane.


Up until the 1970s, it was pretty much standard advice to homeowners to tape plate glass windows to keep them from shattering, but that advice was discredited, and has not been part of hurricane prep advice for 30 years.


Not only does taping windows provide a false sense of security, it can bind shards of flying glass into larger, and more dangerous, projectiles.

Still, the myth hangs on.


A video that I’ve highlighted in the past, from the Pinellas County Office of Emergency Management demonstrates just how useless masking, or duct taping your your windows really is during a storm (be patient, it can take a minute to load).


Tape Strikes Out
Tape Strikes Out

Time: 4 min.

When a storm blows in, you put masking tape on your windows and you're fine right? We'll show you just how wrong that assumption can be.


In May, during National Hurricane Preparedness Week I’ll have a lot more on getting ready for the upcoming season.





But fitting your windows with shutters, or plywood can be time consuming, and is something you should be doing now . . . before the season begins.


To become better prepared as an individual, family, business owner, or community to deal with hurricanes, tornadoes, floods, or any other type of disaster: visit the following preparedness sites.





Tuesday, March 27, 2012

Dysfunctional Science



# 6246



Six weeks ago in Science at the Crossroads, I wrote about the decline the public’s trust in science.


While I cited a number of reasons for this disturbing trend, prime among them has been the abrupt rise in the number of scientific papers that have been retracted sometimes for outright fraud - over the past decade.


Today the editors-in-chief of two prominent journals  made a presentation before a committee of the National Academy of Sciences, where they warn of a growing dysfunction in scientific research, and call this rise in retracted studies a symptom of a much larger problem.


You’ll find detailed and thought provoking editorials authored by Ferric C. Fang, Editor in Chief, Infection and Immunity and Arturo Casadevall, Editor in Chief, mBio on the challenges facing researchers in the current issue of Infection and Immunity (IAI).


The press release from the American Society for Microbiology follows, with the links to a pair of Infection and Immunity editorials on the subject at the end.


Highly recommended.




Has modern science become dysfunctional?

The recent explosion in the number of retractions in scientific journals is just the tip of the iceberg and a symptom of a greater dysfunction that has been evolving the world of biomedical research say the editors-in-chief of two prominent journals in a presentation before a committee of the National Academy of Sciences (NAS) today.


"Incentives have evolved over the decades to encourage some behaviors that are detrimental to good science," says Ferric Fang, editor-in-chief of the journal Infection and Immunity, a publication of the American Society for Microbiology (ASM), who is speaking today at the meeting of the Committee of Science, Technology, and Law of the NAS along with Arturo Casadevall, editor-in -chief of mBio®, the ASM's online, open-access journal.


In the past decade the number of retraction notices for scientific journals has increased more than 10-fold while the number of journals articles published has only increased by 44%. While retractions still represent a very small percentage of the total, the increase is still disturbing because it undermines society's confidence in scientific results and on public policy decisions that are based on those results, says Casadevall. Some of the retractions are due to simple error but many are a result of misconduct including falsification of data and plagiarism.


More concerning, say the editors, is that this trend may be a symptom of a growing dysfunction in the biomedical sciences, one that needs to be addressed soon. At the heart of the problem is an economic incentive system fueling a hypercompetitive environment that is fostering poor scientific practices, including frank misconduct.


The root of the problem is a lack of sufficient resources to sustain the current enterprise. Too many researchers are competing for too little funding, creating a survival-of-the-fittest, winner-take-all environment where researchers increasingly feel pressure to publish, especially in high-prestige journals.



"The surest ticket to getting a grant or job is getting published in a high profile journal," says Fang. "This is an unhealthy belief that can lead a scientist to engage in sensationalism and sometimes even dishonest behavior to salvage their career."


Funding is just one aspect of a very complex problem Casadevall and Fang see growing in the biomedical sciences. In a series of editorials in the journal Infection and Immunity they describe their views in detail, arguing that science is not as healthy as it could be or as it needs to be to effectively address the challenges facing humanity in the 21st century.


"Incentives in the current system place scientists under tremendous stress, discourage cooperation, encourage poor scientific practices and deter new talent from entering the field," they write. "It is time for a discussion of how the scientific enterprise can be reformed to become more effective and robust."


The answers, they write, must come not only from within the scientific community but from society as a whole that has helped create the current incentive structure that is fostering the dysfunction. In the editorials they outline a series of recommended reforms including methodological, cultural and structural changes.


"In the end, it is not the number of high-impact-factor papers, prizes or grant dollars that matters most, but the joys of discovery and the innumerable contributions both large and small that one makes through contact with other scientists," they write. "Only science can provide solutions to many of the most urgent needs of contemporary society. A conversation on how to reform science should begin now."



Copies of the Infection and Immunity editorials can be found online at


Indonesia MOH: Bird Flu Case # 188




# 6245



Overnight the press carried reports (see Indonesia: Sixth H5N1 death this year on Crofsblog) of a new human H5N1 infection out of Indonesia. This time, it involves a 17 year old boy from eastern Lombok island who died on March 9th.


Below you’ll find the the update from the Indonesian Ministry of Health, followed by the update from the World Health Organization.


Bird Flu Case report 188

March 26, 2012 | 9:15 am


Ministry of Health, "Directorate General of disease Control and Environmental Health" announced one new case of H5N1 have been confirmed by the Center for Biomedical and Health Technology, Balitbangkes.


Case on behalf of D (male, 17 years) who Lingsar, West Lombok regency, West Nusa Tenggara Province, is a construction worker. Dated February 28, 2012 symptoms of fever, dated March 1, 2012 cases to the health center outpatient Lingsar, and on March 4, 2012 cases treated at health centers Narmada. On March 7, 2012 cases were referred to the RSU Mataram and treated in hospital. Circumstances of the case got worse and on March 9, 2012 cases died at 23:50 pm.


Epidemiological investigations have been carried into the homes of people and the environment by the Integrated Team Ministry of Health and local health office, obtained the possibility of environmental risk factor is contact with the death of poultry (chicken) in the neighborhood.


With the increase of these cases, the cumulative number of bird flu in Indonesia since 2005 until this news was broadcast on 188 cases with 156 deaths.


Ailing Director General of Control and Environmental Health, Prof. dr. Tjandra Yoga Aditama as the focal point of the International Health Regulations (IHR) has been informed about the case to the WHO.





Avian influenza – situation in Indonesia – update

26 March 2012 - The Ministry of Health of Indonesia has notified WHO of a new case of human infection with avian influenza A(H5N1) virus.


The case is a 17 year-old male from Nusa Tenggara Barat Province. He developed fever on 28 February 2012 and sought treatment on 1 March 2012. His condition deteriorated and he was admitted to a referral hospital but he died on 9 March 2012.


Epidemiological investigation conducted by a team from the health office indicated that there were sudden poultry die-offs in his neighbourhood.


To date, of the 188 cases reported in Indonesia since 2005, 156 have been fatal.




The case fatality rate (CFR) of `known’ cases in Indonesia continues to hover just over 82%, with just 4 of the last 26 cases surviving.


What we don’t know (and is highly contested in some scientific circles) is how many cases we are missing.


While surveillance and reporting almost certainly misses some number of cases (mild and fatal), researchers have turned up very little compelling evidence to indicate that there are a lot of `mild’ cases going uncounted.


Leaving us with a CFR that – while probably artificially high – strongly suggests a significant level of lethality from the H5N1 virus.


Fortunately, the virus remains difficult for humans to acquire, as it is presently far better adapted to avian physiology.


The concern is (as has been demonstrated as being possible in the laboratory), that over time the virus will pick up the mutations it will need to adapt to a human host and spark a pandemic.

Monday, March 26, 2012

When Websites Attack



UPDATED:  I’m pleased to announce that this evening Google’s Webmasters Diagnostics has found Arkanoid’s site clear of any malware, and has removed all warnings.


# 6243




One of the best infectious disease news gatherers in Flublogia is Arkanoid Legent out of Malaysia, whose website normally sits prominently in my side bar.   


This morning, visitors to this site with certain anti-virus software started getting warnings about potentially malicious code emanating from  Arkanoid’s site. This prompted a good deal of back channel communications between me, Arkanoid, and fellow blogger Crof to try to figure out what had happened.




In short order it was determined that the problem did not to have anything to do Arkenoid’s page, but rather with a banner ad to another website (now removed) where some malicious code was apparently embedded.


Arkanoid has submitted his site for a security review to get the `attack site’ designation removed. 


Until this matter is resolved, I’ve inactivated the link to Arkanoid’s site to avoid my visitors getting a warning pop-up, and to prevent the further maligning of an excellent website.


None of this should reflect negatively on Arkanoid’s site. He does a terrific job, and has simply been tarnished by someone else’s misdeeds.


I know how distressing all of this must be for Arkanoid, and I’m hoping that this can get put right as quickly as possible.

Luck Of The Draw



Photo Credit – CDC PHIL


# 6242



While it may seem curious to some, your humble flu blogger here at AFD has never – to his knowledge – ever suffered from a `classic’ bout of flu.


Oh, sure. I’ve had plenty of respiratory infections, albeit mostly upper respiratory. And a couple of times I’ve had what I’ve thought was probably influenza.


But I’ve never had the running fever, crushing body-aches, want-to-die kind of flu that many others seem to report.


I could just be lucky, I guess. 


But I’ve always figured I really wasn’t very susceptible to influenza. That when I’d had the flu, they had been relatively mild cases.  


Of course, I have no way of proving that . . .


But new research published in Nature by Wellcome Trust Sanger Institute lends credence to the idea that some people are genetically more likely to experience severe flu symptoms than others.


First some excerpts from the press release (worth reading in its entirety), then a link to the research article, then I’ll return with some other data suggestive of a genetic susceptibility to influenza.


Genetics of flu susceptibility

Researchers find gene that can transform mild influenza to a life-threatening disease

A genetic finding could help explain why influenza becomes a life-threating disease to some people while it has only mild effects in others. New research led by the Wellcome Trust Sanger Institute has identified for the first time a human gene that influences how we respond to influenza infection.


People who carry a particular variant of a gene called IFITM3 are significantly more likely to be hospitalised when they fall ill with influenza than those who carry other variants, the team found. This gene plays a critical role in protecting the body against infection with influenza and a rare version of it appears to make people more susceptible to severe forms of the disease. The results are published in the journal Nature.


A central question about viruses is why some people suffer badly from an infection and others do not. IFITM3 is an important protein that protects cells against virus infection and is thought to play a critical role in the immune system's response against such viruses as H1N1 pandemic influenza, commonly known as 'swine flu'. When the protein is present in large quantities, the spread of the virus in lungs is hindered, but if the protein is defective or absent, the virus can spread more easily, causing severe disease.

(Continue . . . )


IFITM3 restricts the morbidity and mortality associated with influenza

Aaron R. Everitt,Simon Clare,Thomas Pertel,Sinu P. John,Rachael S. Wash,Sarah E. Smith,Christopher R. Chin,Eric M. Feeley,Jennifer S. Sims,David J. Adams,Helen M. Wise,Leanne Kane,David Goulding,Paul Digard,Verneri Anttila,J. Kenneth Baillie,Tim S. Walsh,David A. Hume,Aarno Palotie,Yali Xue,Vincenza Colonna,Chris Tyler-Smith,Jake Dunning,Stephen B. Gordon,The GenISIS al.

Nature (2012)  doi:10.1038/nature10921



Although this research is the first to identify a specific gene that may make influenza a much more serious illness in some people than others, for some time there’s been evidence suggesting that heritable factors influence how people react to influenza.


In 2008, in the Journal of Infectious Diseases, we saw a study that suggested there might be a heritable susceptibility to death from the influenza virus.


Evidence for a heritable predisposition to death due to influenza.

Albright FS, Orlando P, Pavia AT, Jackson GG, Cannon Albright LA.

Abstract (extract)

Evidence for a heritable contribution to death due to influenza was examined using a resource consisting of a genealogy of the Utah population linked to death certificates in Utah over a period of 100 years. The relative risks of death due to influenza were estimated for the relatives of 4,855 individuals who died of influenza.


Both close and distant relatives of individuals who died of influenza were shown to have a significantly increased risk of dying of influenza, consistent with a combination of shared exposure and genetic effects. These data provide strong support for a heritable contribution to predisposition to death due to influenza.


While interesting, this study doesn’t provide us with a smoking gene.


However, the following year a PLoS ONE  research article doi:10.1371/journal. pone.0004857)  came a bit closer.  


Entitled Host Genetic Background Strongly Influences the Response to Influenza A Virus Infections by Srivastava B, Błażejewska P, Heßmann M, Bruder D, Geffers R, et al., it reports on the results of experiments utilizing seven inbred strains of lab mice that were exposed to influenza A viruses.


From the abstract:


The genetic make-up of the host has a major influence on its response to combat pathogens. For influenza A virus, several single gene mutations have been described which contribute to survival, the immune response and clearance of the pathogen by the host organism.


Granted, mouse models are often useful, but what happens in mice doesn’t always correspond to what happens with human physiology.


And last year, in Host Genetic Susceptibility to Avian Influenza, we saw an analysis of clusters of H5N1 infection in Indonesia that found that young age (under 30) and being a blood relative to the index case in a cluster, were both found to significantly increase the odds of catching the virus.


So there is anecdotal reason to believe that there may be genetic factors involved in either mitigating, or exacerbating, the effects of flu.


Never having suffered a `classic’ bout of flu admittedly gives me some hope that I might have some degree of built-in immunity to a pandemic virus.


But with an emerging or novel flu strain, who knows?


Of course, my good flu fortune may have more to do with my diligence in getting a seasonal flu shot every year, than with any genetic advantage.


But I can hope.

Saturday, March 24, 2012

Tsunami: The Other Coastal Threat





Photo Credit – NTHMP


# 6242



Although storms remain the biggest threat, last year’s devastating combination earthquake/tsunami in Japan has reinforced concerns that many other coastal regions around the world – including those in the United States – are at risk from destructive tidal waves.


While most people automatically think of the Pacific ocean when it comes to America’s vulnerability to tsunamis, the Atlantic seaboard, Florida, and even the Gulf of Mexico are not completely immune to the phenomenon.


A list of known or suspected Atlantic Tsunamis includes:

  • November 1, 1755 - Lisbon, Portugal
  • October 11, 1918 - Puerto Rico
  • November 18, 1929 - Newfoundland
  • August 4, 1946 - Dominican Republic
  • August 18, 1946 - Dominican Republic
  • November 14, 1840 - Great Swell on the Delaware River
  • November 17, 1872 - Maine
  • January 9, 1926 - Maine
  • May 19, 1964 - Northeast USA


  • June 9, 1913 - Longport, NJ
  • August 6, 1923 - Rockaway Park, Queens, NY. An article on triplicate waves."
  • August 8, 1924 - Coney Island, NY. Contains a discussion, “An Observed Tsunami Building In Coastal Waters?"
  • August 19, 1931 - Atlantic City, NJ
  • September 21, 1938 - Hurricane, NJ coast.
  • July 3-4, 1992 - Daytona Beach, FL


The last suspected entry – the infamous Daytona Beach `rogue wave’ of 1992 - was described by witnesses as being between 10 and 18 feet tall, slammed onto a 27 mile stretch of Florida Beaches and smashed hundreds of cars and caused as many as 75 (mostly minor) injuries.


Hawaii and the west coast are, of course, at considerably greater risk due to the seismically active `ring of fire’.  


Perhaps most vulnerable is the Pacific Northwest, where the Cascadia fault line (see Just A Matter Of Time) is believed to have produced tsunamis in the past that rival the tidal waves that struck Japan last year.





All of which helps to explain why the United States government takes the tsunami threat seriously. Tsunamis may not strike often, but when they do, they can be extremely destructive.


This coming week (March 25-31st) is National Tsunami Preparedness Week, and you’ll find information on planned activities in many coastal states on the  National Tsunami Hazard Mitigation Program website.


Other resources to check out include the PHE (Public Health Emergency) Website which includes some videos, along with preparedness resources.




And NOAA’S  National Weather Service  Tsunami Warning Page:




Since tidal waves may arrive with only minutes warning, it is imperative for those living on or near the coast to have a tsunami plan already in place.

That means having a `bug-out bag’ (see NPM11: When You Have To `Get Out Of Dodge’ In A Hurry), an emergency plan (including emergency rendezvous place), and knowing your evacuation routes off the beach.


Tsunamis are relatively rare, but they are just one of many potential threats, which is why most experts recommend an `all threats’ preparedness strategy.


Disasters happen.

And so you need to have adequate emergency supplies (including a good first aid kit), a NOAA weather radio, and a disaster plan, in order to give you and your family the best protection.


Good places to get preparedness information include:






And you can click the following link to search this blog for my PREPAREDNESS ESSAYS.