NIH: News From The Human Microbiome Project

 

Photo Credit HMP

 

# 6385

 

Last year in The Other Reason Not To Abuse Antibiotics I touched briefly on beneficial intestinal bacteria (gut flora or microbiota), and how the use of antibiotics can adversely disrupt their balance.

 

The study of these ubiquitous micro-organisms that reside not only in our intestines, but on our skin, in our nasal passages, oral cavities, gastrointestinal tract, and urogenital tract has gained momentum over the past several years.

 

One of the big reasons is the NIH sponsored Human Microbiome Project, which defines their goal as:

 

 

The Common Fund's Human Microbiome Project (HMP) aims to characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease. HMP includes the following initiatives.

 

 

Today, in advance of the publication today and tomorrow of a number of research articles in PLoS and in the journal Nature, we’ve a couple of lengthy press releases describing this international project’s recent accomplishments, along with an announcement on the PLoS Blog of the availability of this collection.

 

 

First, from the NIH – news that researchers have defined the normal bacterial makeup of the human body.

 

 

NIH Human Microbiome Project defines normal bacterial makeup of the body

Genome sequencing creates first reference data for microbes living with healthy adults

Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival. For the first time, a consortium of researchers organized by the National Institutes of Health has mapped the normal microbial makeup of healthy humans, producing numerous insights and even a few surprises.

 

Researchers found, for example, that nearly everyone routinely carries pathogens, microorganisms known to cause illnesses. In healthy individuals, however, pathogens cause no disease; they simply coexist with their host and the rest of the human microbiome, the collection of all microorganisms living in the human body. Researchers must now figure out why some pathogens turn deadly and under what conditions, likely revising current concepts of how microorganisms cause disease.

 

In a series of coordinated scientific reports published on June 14, 2012, in Nature and several journals in the Public Library of Science (PLoS), some 200 members of the Human Microbiome Project (HMP) Consortium from nearly 80 universities and scientific institutions report on five years of research. HMP has received $153 million since its launch in fiscal year 2007 from the NIH Common Fund, which invests in high-impact, innovative, trans-NIH research. Individual NIH institutes and centers have provided an additional $20 million in co-funding for HMP consortium research.

 

“Like 15th century explorers describing the outline of a new continent, HMP researchers employed a new technological strategy to define, for the first time, the normal microbial makeup of the human body,” said NIH Director Francis S. Collins, M.D., Ph.D. “HMP created a remarkable reference database by using genome sequencing techniques to detect microbes in healthy volunteers. This lays the foundation for accelerating infectious disease research previously impossible without this community resource.”

(Continue . . . )

 

 

In another press release from the University of North Carolina at Charlotte, we get details on how this research was conducted, and the surprising individuality and diversity among health human biomes.

 

 

Human Microbiome Project finds vast individuality in healthy human bacterial populations

(EXCERPT)

To define the normal human microbiome, HMP researchers sampled 242 healthy U.S. volunteers (129 male, 113 female), collecting tissues from 15 body sites in men and 18 body sites in women (including three vaginal sites). Researchers collected up to three samples from each volunteer at sites such as the mouth, nose, skin (two behind each ear and each inner elbow),and lower intestine (stool).

Where doctors had previously isolated only a few hundred bacterial species from the body, HMP researchers now calculate that more than 10,000 species occupy the human ecosystem. Moreover, researchers calculate that they have found between 81 and 99 percent of all the genuses of microorganisms in healthy adults.

Defining "a" human biome, however, can be difficult, as HMP researchers found immense variation in bacterial communities, both in bacterial diversity and in bacterial group abundances -- variation that includes population differences both between areas in each body and between similar areas in different bodies.

Each body site can be inhabited by organisms as different as those in the Amazon Rainforest and the Sahara Desert. Further, these sites on different individuals are populated with different assemblages of bacteria, or with some of the same bacteria, but in markedly different proportions.

(Continue . . . )

From the Public Library of Science Blog we get details on this expanding collection of research.

 

Announcing the Human Microbiome Project Collection

Posted on June 13th, 2012 by Jen Laloup

For the first time, a consortium of researchers has mapped the full community of microbes that inhabit various parts of the healthy human body. Many of these findings will be published today in a new PLoS collection. The PLoS Human Microbiome Project Collection consists of articles from the project’s consortium members, who generate, leverage, and explore microbiome analytical techniques. The articles have been culled from PLoS ONE, PLoS Genetics, and PLoS Computational Biology with more being added to the collection as they are published.

(Continue . . .)

 

The PLoS Microbiome collection features 13 new research papers published today. To access these papers, please visit:

 

PLoS Collections: The Human Microbiome Project Collection (2012) www.ploscollections.org/hmp

»» Read More

Nature: Bird Flu Research Oversight

 

BSL-4 Lab Worker - Photo Credit –USAMRIID  

# 6342

 

From the journal Nature today, a detailed look by Brendon Maher at how the NSABB examined the Kawaoka and Fouchier H5N1 research papers, and the long, tortuous road towards a final decision on their publication.

 

For those who did not follow this story, briefly:

 

In September of 2011, one of the best known flu researchers in the world - Ron Fouchier of Erasmus Medical Centre in Rotterdam - announced at a scientific conference that he’d managed to turn H5N1 into a virulent, and easily transmissible (among ferrets, anyway) pathogen.

 

(You can read about this work in Katherine Harmon’s Sci-Am article and in a follow up to this story in New Scientist: Five Easy Mutations.)

 

Halfway across the world, Yoshihiro Kawaoka, a highly respected virologist at the University of Wisconsin-Madison School of Veterinary Medicine announced the creation of a comparable H5N1 super flu at roughly the same time.

 

Within weeks biosecurity experts began to question whether scientists should even be tinkering with this particularly lethal flu strain, and whether (or how) those results should be published.

 

The NSABB was tasked with reviewing these projects, and making a recommendation to the United States government.

 

After first recommending that the full studies not be published, the NSABB – under mounting pressure from a number of directions – reconsidered their decision in light of `revised and clarified’ manuscripts from Fouchier, and green-lighted their publication.

 

Brendon Maher explores the process by which these disparate decisions were reached, and the lingering concerns held by many involved in. 

 

This is an important story, and well worth reading in its entirety, so follow the link below:

 

 

Nature | News Feature

Bird-flu research: The biosecurity oversight

The fight over mutant flu has thrown the spotlight on a little-known government body that oversees dual-use research. Some are asking if it was up to the task.

• Brendan Maher

23 May 2012

»» Read More

Nature Publishes The Kawaoka H5N1 Study

 

BSL-4 Lab Worker - Photo Credit –USAMRIID

 

# 6312

 

 

Although it was Ron Fouchier’s announcement last September (see New Scientist: Five Easy Mutations) of his successful manipulation of the H5N1 virus to make it transmissible among ferrets that set off biosecurity alarm bells (see NPR: Bio-Terrorism Concerns Over Bird Flu Research) and instigated an international debate, in a laboratory halfway around the world Dr. Yoshiro Kawaoka was quietly duplicating the feat.

 

Today (the embargo having lifted at 1pm) the journal Nature publishes Kawaoka’s study, which details how he created a modified H5N1 – H1N1 hybrid that transmits via respiratory droplets among ferrets.

 

While its virulence in ferrets was reduced over that of its parental H5N1 virus (exactly why is unknown), the big news is that it only took the introduction of 4 mutations into the H5N1’s hemagglutinin (HA) to allow it to bind efficiently to the alpha (2-6) sialic acid receptors found in ferret (and human) upper respiratory tracts.

 

Three of these mutations were directly involved in the binding to the a2,6 receptor cell, while the 4th stabilized the virus to fuse with receptor cells at pH levels typically found in the upper respiratory tract. 

 

An affinity for a2,6 receptor cells has long been thought vital for the virus to adapt to humans, but this 4th mutation - that facilitates virus-cell fusion - may prove equally important.

 

Given its highly public and bumpy road to publication, Kawaoka’s study (see below) is certain to receive an inordinate amount of scrutiny and review over the next couple of days.

 

 

Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to areassortant H5 HA/H1N1 virus in ferrets

 

doi:10.1038/nature10831

Masaki Imai, Tokiko Watanabe, Masato Hatta, Subash C. Das, Makoto Ozawa, Kyoko Shinya, Gongxun Zhong, Anthony Hanson, Hiroaki Katsura, Shinji Watanabe, Chengjun Li , Eiryo Kawakami , Shinya Yamada, Maki Kiso5,Yasuo Suzuki , Eileen A. Maher, Gabriele Neumann & Yoshihiro Kawaoka

 

Kawaoka’s 11-page study is, as you might imagine, highly technical and may prove tough sledding for those without a solid background in virology.

 

Nature published a 2-page synopsis by Hui-Ling Yen & Malik Peiris that helps to explain some of the details, but this is a pay-to-view article.

 

 

Bird flu in mammals

An engineered influenza virus based on a haemagglutinin protein from H5N1 avian influenza, with just four mutations, can be transmitted between ferrets, emphasizing the potential for a human pandemic to emerge from birds. 

 

 

According to Malik Peiris, this study reaffirms the pandemic potential of the H5N1 virus, and reinforces the need for better surveillance of the virus in the wild.

 

While Kawaoka identified several mutations in the H5 HA that allowed the virus to bind to a2,6 receptors there are likely other combinations that could lead to greater transmissibility.

 

For the best all-around coverage of this story, we can always rely on Helen Branswell of The Canadian Press. Helen has just posted the following article on this research’s publication.

 

 

Bird flu study: Three mutations might give virus ability to transmit to humans

By: Helen Branswell, The Canadian Press

 

 

There will, undoubtedly, be a large number of stories and opinion pieces regarding the publication today of Kawaoka’s research.

 

Already I note  that Vincent Racaniello has blogged on this publication:

 

Kawaoka paper published on aerosol transmission of H5 influenza virus in ferrets

2 May 2012

Meanwhile Laurie Garrett  takes a more cautionary route in:

 

Manmade H5N1 Paper Finally Published, And Worrying

 

 

I’ll update this blog with more links to articles and opinion pieces on this research later today or tomorrow.

»» Read More

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)

doi:10.1038/483534a

 

 

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.

»» Read More

Declan Butler On the CFR Of H5N1

 

# 6141

 

 

Declan Butler, who is a senior reporter Nature.com, was one of the first journalists to call attention to the H5N1 virus.  He holds a degree in biology from Queen's University, Belfast, has a PhD from the University of Leeds, and writes on a variety of scientific topics.

 

The CFR (Case Fatality Ratio) of the H5N1 virus – which hovers around 60% of known cases - has been the subject of considerable discussion over the years, and is currently front and center in the recent debate over H5N1 research in ferrets.

 

Some scientists maintain that a great many `mild’ cases go undetected, and that the true CFR is far lower (perhaps `orders of magnitude lower’) than the official numbers would indicate (see Vincent Racaniello’s argument Should we fear avian H5N1 influenza?). 

 

As we saw in a CIDRAP article last week by Robert Roos (Undetected H5N1 cases seem few, but questions persist), not everyone buys into that theory.

 

Today Declan Butler talks to a number of experts (including Malik Peiris and Jeremy Farrar), who say they’ve not found much evidence to support a claim that we are missing a lot of `mild’ cases.

 

While the true CFR may be far lower than 59%, many experts believe this virus is fully capable of producing a pandemic that could far exceed what we saw with the 1918 Spanish Flu.

 

Very much worth reading, so follow the link to:

 

 Nature | News

Death-rate row blurs mutant flu debate

Even if a 59% mortality rate for H5N1 is too high, the virus could still cause a flu pandemic more serious than that of 1918.

Declan Butler

13 February 2012

(Continue . . . )

»» Read More

Nature Editorial: Facing Up To Flu

 

BSL-4 Lab Worker - Photo Credit –USAMRIID

 

 

# 6130

 

Tying in with my last post (see Declan Butler: Lab flu may not aid vaccines), we’ve an editorial appearing today in Nature that calls into question the short-term benefits of so-called  `dual use’ H5N1 research.

 

Follow the link to read:

 

Nature | Editorial

Facing up to flu

Nature 482,131

(09 February 2012) doi:10.1038/482131a

Published online 08 February 2012

The potential for mutant-flu research to improve public health any time soon has been exaggerated. Timely production of sufficient vaccine remains the biggest challenge.

(Continue . . .)

 

 

I expect that we’ll see vigorous counterpunching on this issue in the not too distant future as both sides prepare for the meeting in Geneva next week.

 

Stay tuned.

 

The stakes here are extraordinarily high, the issues are complex, and I expect no shortage of fireworks.

»» Read More

Nature: Yoshihiro Kawaoka Talks About His H5N1 Research

 

BSL-4 Lab Worker - Photo Credit –USAMRIID

 

#  6101

 

Although two scientists, working independently and a half-a-world-apart have recently created a more transmissible version of the H5N1 virus, it has been the work of Ron Fouchier at Erasmus University that has garnered the most press.

 

The reason is pretty simple.

 

Fouchier announced his findings at a scientific conference late last summer (see Katherine Harmon’s Sci-Am article and in a follow up to this story in New Scientist: Five Easy Mutations), while Yoshihiro Kawaoka has – until now - refrained from discussing his work publicly.

 

Today in a Nature commentary, flu virologist Yoshihiro Kawaoka breaks his silence and talks about his research into the H5N1 virus, and why such research should continue.

 

H5N1: Flu transmission work is urgent

• Yoshihiro Kawaoka

Nature (2012)

doi:10.1038/nature10884 Published online

25 January 2012

Yoshihiro Kawaoka explains that research on transmissible avian flu viruses needs to continue if pandemics are to be prevented.

 

Taking a different approach than that used by Fouchier, Kawaoka created a reassortant virus combining H5N1 and the 2009 H1N1 virus, which while transmissible between ferrets, was no more pathogenic than regular flu.

 

As you might expect, Helen Branswell is already all over this story, and you can find her take on it at:

 

The Canadian Press - ONLINE EDITION

Researcher at heart of bird flu studies controversy reveals details of his findings

By: Helen Branswell, The Canadian Press

»» Read More

Nature: 10 Expert Opinions On The H5N1 Research Dilemma

 

 

# 6077

 

The Journal Nature, which has been covering the H5N1 research controversy since the issue erupted, has solicited the opinions of 10 experts in influenza research on how to deal with the current H5N1 research controversy.

 

As you will find, the issues are complex, and answers that are going to satisfy everyone (or perhaps, anyone) are going to be very hard to find.

 

Follow the link below to read:

 

Preventing pandemics: The fight over flu

Nature (2012)  doi:10.1038/481257a

Published online 15 January 2012

A proposal to restrict the planned publication of research on a potentially deadly avian influenza virus is causing a furor.

Ten experts suggest ways to proceed.

 

You’ll find opinions voiced by such influenza luminaries as:

 

Ron Fouchier & AB Osterhaus

John Steinbruner

Kwok-Yung Yuen

D. A. Henderson

Lynn Klotz & Ed Sylvester

Jeffery K. Taubenberger

Richard H. Ebright

David L. Heymann

 

 

 

Nature has also set up a special portal to allow readers to access the growing backlog of news and opinion surrounding this issue.

 

Mutant flu

Scientists have created a form of the H5N1 avian flu virus that is transmissible between mammals, raising fears that it could trigger a human pandemic if it escapes from the lab - either through accidental release or as part of a bioterror attack. As debate rages over how much of the research should be published, and whether there is sufficient oversight of such work, you can follow all Nature's coverage of the issue here.

 

»» Read More

You Say You Want An Evolution?

 

 

 

# 5576

 

 

One of the topics we return to in this blog with some frequency is the potential for pigs – which are susceptible to a variety of swine, human, and avian influenza viruses - to serve as `mixing vessels’ and to generate new influenza strains.

 

Since pigs can be infected by more than one flu virus at the same time, the potential exists for two viruses to swap genetic material (reassort), resulting in a new hybrid strain.

 

The pandemic virus that emerged in the spring of 2009 was the end product of several influenza strains that had kicked around the world’s swine population for many years, trading bits of genetic material back and forth, until they produced a version capable of jumping to humans.

 

In the not-too-distant past, pigs were usually raised and slaughtered locally.

 

Over the past couple of decades, however, the cross country - and even international – shipping of live hogs has become a big business.  

 

According to Dr. Michael Greger’s excellent Flu Factories video presentation, pigs raised in the United States often travel hundreds of miles `on the hoof’, with many being `bred in North Carolina,  fattened in the corn belt of Iowa, but slaughtered in California’.

 

Which means that a swine virus that emerges in North Carolina could easily spread across the nation, carried either by live pigs, or on contaminated transport vehicles.

 

Internationally, live hogs are often shipped for breeding purposes, to inject genetic diversity into local herds to improve the breed.

 

Unfortunately, this practice has also increased viral diversity as well, introducing North American and European flu stains to places like China.

 

All of which serves as prelude to a study which was published yesterday in the Journal Nature, that takes the most extensive look to date at the introduction and evolution of swine flu viruses in China over the past 12 years (supplemented by data going back 34 years).

 

This report has an impressive pedigree, including such familiar names in the world of influenza virology as Kennedy F. Shortridge, Richard J. Webby, Robert G. Webster, Yi Guan  and  J. S. Malik Peiris.

 

 

Long-term evolution and transmission dynamics of swine influenza A virus

Dhanasekaran Vijaykrishna,Gavin J. D. Smith, Oliver G. Pybus, Huachen Zhu, Samir Bhatt, Leo L. M. Poon, Steven Riley, Justin Bahl, Siu K. Ma, Chung L. Cheung, Ranawaka A. P. M. Perera, Honglin Chen, Kennedy F. Shortridge, Richard J. Webby, Robert G. Webster, Yi Guan & J. S. Malik Peiris

 

 

Although the study is, lamentably, not open access, we’ve a number of resources giving us overviews of what was found.

 

First stop is a press release from the NIH/NIAID, which partially funded this work.

 

Evolution of swine flu viruses traced in long-term study

NIH-funded project yields baseline for better understanding of human influenza

Although swine influenza viruses usually sicken only pigs, potentially one might also spark a pandemic in people, as occurred with the 2009 H1N1 influenza virus. Because few long-term studies have surveyed flu viruses in swine, however, gaps exist in what is known about the evolution of swine influenza viruses and the conditions that enable a swine virus to infect humans and cause disease.

 

In new research reported in Nature, scientists analyzed the genetic makeup of more than 650 influenza viruses isolated during the systematic surveillance of pigs slaughtered in Hong Kong between 1998 and 2010. When the investigators supplemented this information with additional data stretching back 34 years, they could discern when specific subtypes of flu virus—including strains that had previously infected only birds or humans—first appeared in Hong Kong swine.

 

The researchers also traced the relative abundance of each of three major swine influenza virus lineages: classical, Eurasian avian-like and triple reassortant. Examples of all three of these long-established virus family lineages were found in varying proportions in samples gathered between 2002 and 2009. Before 2003, the classical lineage predominated; by 2005, the Eurasian lineage, first detected in 2001, had become most common. The most recent samples contain not only viruses from the three previously established swine lineages, but also from the new 2009 H1N1 strain. It is not yet known whether the new pandemic strain will permanently establish itself in swine.

 

According to this analysis, the three swine influenza virus lineages have crossed geographic boundaries, including continents. Such extensive co-circulation of multiple strains facilitates gene-swapping between viruses, note the researchers, and they recommend continued surveillance of swine influenza genetic diversity to better understand how this process might give rise to variants with the potential to cause human flu epidemics. Their baseline data not only show the evolutionary dynamics in swine influenza, but also highlight ways in which swine flu viruses might most readily adapt to cause infection in people.

 

CIDRAP , as part of their daily news scan, has a brief report on this as well (excerpted, and slightly reformatted for readability).

 

Imports helped swine flu in Hong Kong pigs to diversify

Importing pigs from Europe and North America over the past 30 years appears to have increased the genetic diversity of swine influenza in Hong Kong pigs through gene reassortment, according to a study today in Nature.

 

<SNIP>

 

The authors write, "Intercontinental virus movement has led to reassortment and lineage replacement, creating an antigenically and genetically diverse virus population."

 

Vijaykrishna Dhanasekaran, PhD, of Duke University, a study co-author, said the increased genetic diversity "means that the repertoire of viruses that humans are in contact with every day has increased, and this may lead to a higher likelihood of swine-to-human transmission, although the risk remains unquantified."

 

 

Duke University Medical Center – a participant in this study – has also put out a press release.

 

 

Long-term study of swine flu viruses shows increasing viral diversity

DURHAM, NC and SINGAPORE – Increased transportation of live pigs appears to have driven an increase in the diversity of swine influenza viruses found in the animals in Hong Kong over the last three decades, according to a new study.

 

In the longest study of its kind, Duke-NUS Graduate Medical School researchers found that swine viruses crossed geographic borders and mixed with local viruses, increasing their diversity.

 

(Continue . . . )

 

 

While this data is both vital and welcome, for most of the developing world, little or no viral surveillance of pigs takes place.

 

Even in the U.S. some hog farmers are reluctant to allow their herds to be tested (see Swine Flu: Don’t Test, Don’t Tell) out of fears that the discovery of a new swine flu virus would depress pork sales.

 

Some will only consent to anonymous testing, which limits the CDC’s ability to investigate cases.

 

Every once in awhile we get a report from somewhere in the world that a human has been infected with a novel influenza virus, usually of swine, avian - or quite often - mixed origin.  A few examples:

 

China: Single Novel Swine Flu Infection Reported

North America Influenza Surveillance - Week 4

CDC: Another Novel H3N2 Isolate

 

Rarely, as in the case of the 2009 swine flu virus, a novel strain adapts well enough to humans to spread efficiently through the population.

 

Most of the time, however, these are one-off type infections that are directly transmitted from an animal (pig, bird) to a single human.  Secondary transmission of the virus to others probably occurs, but only rarely and in a limited fashion.

 

But this serves as a constant reminder that nature’s laboratory is open 24/7, and viral evolution proceeds at remarkable speed.

 

For more background on influenza in swine, and the risks of reassortment, you can’t do better than  Helen Branswell’s excellent Scientific American article from last December called Flu Factories, or her SciAm Podcast.

 

You may also wish to revisit.

 

Hong Kong: Influenza Surveillance In Pigs

EID Journal: Swine Flu Reassortants In Pigs

The (Swine) Influenza Reassortment Puzzle

If You’ve Seen One Triple Reassortant Swine Flu Virus . . .

»» Read More

Declan Butler On Haiti’s Cholera Epidemic

 

 

 

# 5083

 

 

A lot of my readers are no doubt familiar with Nature News senior reporter Declan Butler for, among many accomplishments, his early work in bringing the avian flu story to the public.

 

But Butler is hardly a Johnny one-note. He holds a PhD in marine biology from the University of Leeds, and writes on a variety of scientific issues.

 

Today he brings us background and sobering analysis of the potential impact of the cholera epidemic on Haiti’s population over the next year or so.

 

A hat tip to David Dobbs for retweeting this link.

 

I’ve just posted his lede.

 

Follow the link to read it in its entirety.  As with practically anything Butler writes, this is highly recommended.

 

 

Cholera tightens grip on Haiti

Those tackling the epidemic are struggling to keep pace with an escalating crisis.

Declan Butler

As cholera rampages through Haiti, some epidemiologists are warning that the country could face more than half a million cases over the coming year. Yet tracking and treating the disease is proving increasingly difficult as civil unrest grips the county.

(Continue. . . )

»» Read More

Experts Weigh In On Allegations Against The WHO

 

# 4633

 

 

A hat tip to Crof over at Crofsblog for picking up this story while I was away from my computer, penned by Declan Butler of Nature News.

 

Included are responses from such heavy hitters as Michael Osterholm of CIDRAP, Virologist Albert Osterhaus of at Erasmus Medical Centre in Rotterdam, Epidemiologist David Ozonoff of the Boston University School of Public Health, and Marc Lipsitch, an epidemiologist at Harvard School of Public Health.

 

Frankly, there’s so much quotable material in this article, rather than excerpt any of it, I will just direct you to the link so you can read it for yourself.

 

 

Published online 8 June 2010 | Nature | doi:10.1038/465672a

News

Flu experts rebut conflict claims

Reports throw unsubstantiated suspicion on scientific advice given to the World Health Organization.

»» Read More

Declan Butler: Portrait Of A Year Old Pandemic

 

# 4515

 

Declan Butler, senior reporter for Nature and a blogger in his own right,  was one of the first journalists to begin covering the avian flu threat back in 2004, and it was his work that helped inspire me to begin this blog.  

 

But hey, you really shouldn’t blame him . . .

 

But I digress.  Today Butler brings us a portrait of the H1N1 pandemic on its first birthday.  

 

I’ll do the wise thing here, and simply give you the link and step out of the way.

 

 

Portrait of a year-old pandemic

'Swine flu' isn't over yet, but it already holds lessons for the future.

Declan Butler

 

One year ago this month, the world watched with trepidation as a novel influenza A virus, to which the global population had little or no immunity, emerged in Mexico and the United States. In the weeks that followed, the H1N1 'swine flu' virus spread rapidly to countries worldwide, leading the World Health Organization (WHO) on 11 June 2009 to officially declare the first flu pandemic in more than 40 years. Nature looks at the lessons learnt from H1N1, and how they will help scientists and health authorities to handle the next flu pandemic.

 

(Continue . . .)

»» Read More

Research: How Flu Succeeds

 

 

# 4182

 

 

Perhaps the biggest `up side’ to this, or any pandemic, is the increase in research into the science of virology and influenza viruses.   After decades of neglect, influenza is suddenly a `hot’ topic for investigation.

 

Vaccine technologies, new antivirals, even NPI’s (Non Pharmaceutical Interventions) are getting closer scrutiny.   While many of these advances won’t do much for us with this pandemic virus, they hold promise for the next pandemic . . . or the one after that.

 

As incredible as it sounds, there is still much we don’t know about how influenza works in the body, how it is spread, or why some people get very ill while others can be infected without symptoms.

 

But there are research centers around the world working to answer these, and other questions.   

 

Today we get a fascinating look at some of the research being conducted by the Burnham Institute of Medical Research, Mount Sinai School of Medicine ,the Salk Institute for Biological Studies and the Genomics Institute of the Novartis Research Foundation (GNF) who have identified 295 Host factors that help flu throughout its lifecycle.

 

Below you’ll find excerpts from the Burnham press release.  There is also a short (2 minute) video on the website explaining about some of this research.

 

The full findings are published the Journal Nature, and I’ve provided a link and an excerpt from the abstract, as well.

 

 

 

How Flu Succeeds

Investigators identify host factors that help multiple influenza strains thrive and could be targeted for new antivirals

LA JOLLA, Calif., December 21, 2009 -- Investigators at Burnham Institute for Medical Research (Burnham), Mount Sinai School of Medicine (Mount Sinai), the Salk Institute for Biological Studies (Salk) and the Genomics Institute of the Novartis Research Foundation (GNF) have identified 295 human cell factors that influenza A strains must harness to infect a cell, including the currently circulating swine-origin H1N1. The team also identified small molecule compounds that act on several of these factors and inhibit viral replication, pointing to new ways to treat flu. These findings were published online on December 21 in the journal Nature.

 

 

Influenza A virus contains only enough genetic information (RNA) to produce 11 proteins and must co-opt host cellular machinery to complete its life cycle. Sumit Chanda, Ph.D., of Burnham, Megan Shaw, Ph.D., of Mount Sinai, John Young, Ph.D., of Salk, Yingyao Zhou, Ph.D., of GNF and others used RNAi screening technology to selectively turn off more than 19,000 human genes to determine which human factors facilitate viral entry, uncoating, nuclear import, viral replication and other necessary functions of the virus.

 

“Because influenza mutates so readily, it has become a moving target for therapeutic intervention, making it difficult to treat circulating strains, including the H1N1 swine flu,” said Dr. Chanda. “As a result, there is now widespread resistance to two classes of antiviral drugs. However, by targeting more stable human host factors, we may be able to develop therapies that prevent or treat a variety of influenza A strains and are more likely to maintain their effectiveness.”

 

“This study has provided us with crucial knowledge of the cellular pathways and factors the influenza virus exploits to replicate” added Dr. Shaw. “Each of these represents an ‘Achilles heel’ of the virus and vastly increases the number of potential targets for new influenza antiviral drugs.”

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The Nature journal article. doi:10.1038/nature08699

 

Human host factors required for influenza virus replication near-final version

Renate König^1,9, Silke Stertz^4,9, Yingyao Zhou⁷, Atsushi Inoue¹, H. -Heinrich Hoffmann⁴, Suchita Bhattacharyya², Judith G. Alamares⁴, Donna M. Tscherne⁴, Mila B. Ortigoza⁴, Yuhong Liang⁴, Qinshan Gao⁴, Shane E. Andrews³, Sourav Bandyopadhyay⁸, Paul De Jesus¹, Buu P. Tu⁷, Lars Pache¹, Crystal Shih¹, Anthony Orth⁷, Ghislain Bonamy⁷, Loren Miraglia⁷, Trey Ideker⁸, Adolfo García-Sastre^4,5,6, John A. T. Young², Peter Palese^4,5, Megan L. Shaw^4,9 & Sumit K. Chanda^1,9

 

 

Influenza A virus is an RNA virus that encodes up to 11 proteins and this small coding capacity demands that the virus use the host cellular machinery for many aspects of its life cycle¹.

 

 

Knowledge of these host cell requirements not only informs us of the molecular pathways exploited by the virus but also provides further targets that could be pursued for antiviral drug development. Here we use an integrative systems approach, based on genome-wide RNA interference screening, to identify 295 cellular cofactors required for early-stage influenza virus replication.

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Nature: One killer virus, three key questions

 

 

# 3994

 

Nature.com has been on the forefront of covering both avian and (now) H1N1 pandemic flu for years.  Declan Butler was writing about H5N1 more than 5 years ago, and truth be told, it was his blog that got me really interested in the subject.

 

You’ll find probably a dozen of his articles referenced in this blog, many of those coming since the emergence of the H1N1 virus last spring. 

 

Today Butler, along with Nature feature writer Brendan Maher, take a hard look at 3 crucial questions regarding the H1N1 `swine’ flu virus.

 

How the virus kills?

How it spreads?

Chances that the pandemic virus will reassort?

 

There's way too much here to excerpt, and so I’ll just tell you to go read it. 

 

Published online 11 November 2009 | Nature 462, 154-157 (2009) | doi:10.1038/462154a

Swine flu: One killer virus, three key questions : Nature News

As the world mobilizes against the H1N1 flu pandemic, researchers are working to answer pressing questions about the virus. Brendan Maher visited pathologists at the US Centers for Disease Control and Prevention who are looking at how the virus kills, and a New York laboratory that is testing how it spreads. Declan Butler spent time at a French biosafety level-4 facility where researchers are working out the chances that the pandemic virus will reassort with the H5N1 avian flu virus.

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