Inside The New Flu Virus

May 8, 2009

Health & Science
Inside The New Flu Virus

by Richard Knox

Listen Now [4 min 23 sec]

May 7, 2009 · A crash effort to analyze the genes of the swine flu virus has revealed that it first emerged in humans last year — most likely last fall.

“The consistent range we’re getting out is the second half of last year — between June and December,” says Oliver Pybus of Oxford University. “The best estimate is the middle of that range, kind of September.”

That means the newly recognized virus has been hiding in plain sight for the past eight months or so. Researchers say it probably had been circulating in Mexico and causing disease there, but its presence was masked by cases of regular flu and the absence of lab tests to identify the newcomer.

A Dizzyingly Complex Virus

Genetic analysis of the swine flu virus is proceeding at a furious pace, abetted by the Internet. The research is not only yielding early insights about the virus’s lineage and age, but scientists say the work will also be crucial in tracking how the virus is evolving and what sort of threat it may represent over the coming months.

Pybus is one of 11 scientists around the world who’ve been digging through genetic data on thousands of animal and human flu viruses and sharing it with each other on a new swine flu wiki. This is the fastest a new flu virus has ever been identified and placed on a family tree that’s dizzyingly complex.

“This has got to be the way this happens from this point forward,” says Michael Worobey of the University of Arizona, another member of the spontaneous new collaboration, which includes groups from Hong Kong to Edinburgh and Tucson, Ariz., to Gainesville, Fla.

Where Did The Virus Come From?

The effort has already shed considerable light on where the new-found virus came from and over what period it evolved. Its great-grand-daddy was what flu scientists call a “triple reassortant” — a three-fer virus made up of genes from a seasonal human flu virus of the H3N2 family, a North American bird virus and a classic swine virus.

The three separate viruses got together in a pig somewhere. When all three ancestor viruses infected the same pig cell, that enabled them to swap genes, a trick flu viruses specialize in.

“Pigs are special because they are easily infected with swine viruses, avian viruses and human viruses,” says Joan Nichols of the University of Texas in Galveston. “That makes pigs a mixing pot.” The pot keeps boiling, genetically speaking, because flu viruses are notoriously mistake-prone as they replicate within a bird or mammalian “host.”

“This virus doesn’t have a proof-reading mechanism, so it makes a lot of sloppy little mistakes along the way,” Nichols says. Some viruses with those “mistakes” survive and thrive because the mutations allow them to spread more efficiently or infect another species. Other mutations cause more severe disease in the virus’s hosts.

A Flu Stew

Scientists say the swap meet that gave rise to the newly discovered swine flu virus happened 10 or 20 years ago. That “triple reassortant” spread among swine for years, but it wasn’t yet able to spread among people. It acquired that ability only last year, when the old “triple reassortant” combined again with two other pig viruses that circulated in North American and Eurasian swine.

That created the virus that’s currently bedeviling the world. The new collaborative group calls it A/California/04/2009 because it was first identified near San Diego in April 2009. It is, in fact, mostly a swine virus with human and bird elements.

Pybus says it really should be called the “gallimaufry” virus. That’s a 16th century French word that means “stew” or “hodgepodge.”

Finding Clues For Next Flu Season

Scientists will track genetic changes and correlate them with the kinds of disease it causes in the Southern Hemisphere, where the flu season begins this month. So far the swine flu virus has begun to turn up in Costa Rica, Colombia, El Salvador and Guatemala.

“We’re going to be actively monitoring what it does as it moves through the population,” says Joan Nichols. “As it turns around and comes back to us in the fall, we’ll know much more about it.”

If it starts causing severe and fatal disease at a high rate in the Southern Hemisphere, that will be obvious enough. Scientists will quickly analyze viruses from such cases to see if they can identify the genetic changes that correlate with increase virulence.

But unfortunately, the absence of such an obvious signal this summer may not mean the virus won’t evolve into a pandemic killer in the fall. That’s because researchers know relatively little about the genes that confer virulence.

Jeffrey Taubenberger of the National Institute of Allergy and Infectious Diseases knows as much about virulence in flu viruses as anyone. He led an effort to reconstruct the killer virus of 1918, which has enabled scientists to probe what made it so dangerous.

Taubenberger says virulence doesn’t appear to reside in a particular gene mutation. Instead it comes from the interaction of still-unknown genetic elements, which he calls “a constellation effect.”

“Virulence and other behaviors are totally dependent on the overall makeup of the virus,” Taubenberger says.

Nichols says the only solution is to watch the newly discovered virus obsessively in the coming months. “Remember,” she says, “this virus hasn’t stopped. It’s just begun.”
[end quote]

Snowy Owl

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Keiji Fukuda: said it was “quite likely” the WHO would declare a pandemic in the near future

May 7, 2009

Official says H1N1 could infect third of world

Reuters
May 7, 2009 at 9:18 AM EDT

BANGKOK — A third of the world’s population could be infected by the H1N1 flu virus in the next year, a top UN health official said today, urging Asian governments to stay alert for a potentially wider pandemic.

Keiji Fukuda, acting assistant director-general for the World Health Organization (WHO), also said it was “quite likely” the WHO would declare a pandemic in the near future but a final decision had not been made.

“This is a disease that could potentially infect a third or more of the world’s population in the next several months, in the next year,” Mr. Fukuda told Asian health officials meeting in Bangkok by conference call from Geneva.

He added that “even if the illnesses appear relatively mild on a global level, the global population level adds up to enormous numbers.”

Health ministers from Japan, China, South Korea and the 10-member Association of South East Asian Nations (ASEAN) will attend the Bangkok meeting on Friday to discuss efforts to co-ordinate their fight against the virus.

Thai soldiers and police imposed tight security around the meeting venue today to prevent any recurrence of the violence that forced an Asian leaders’ summit to be cancelled in April.

Also known as swine flu, the virus, which has killed 44 people in Mexico and the United States and spread through Europe, has not appeared widely in Asia so far. There are five confirmed cases in New Zealand, three in South Korea and one in Hong Kong.

After bouts with SARS and bird flu in recent years, Asian health officials said they were better prepared to handle a pandemic, with stronger surveillance systems, laboratories and stockpiling of antiviral drugs.

But David Nabarro, the UN influenza co-ordinator, worried governments might get complacent because many people in harder-hit countries had experienced only mild symptoms from the flu and recovered without medicine.

He said the most serious flu pandemic of modern times, which killed some 40 million people in 1918-19, started with a milder early wave of infections. “We have to maintain vigilance and understand that the virus we are dealing with could easily change and become much more ferocious. We cannot let down our guard, regardless of what we are seeing at the moment,” Mr. Nabarro told the conference.

Mr. Fukuda said there was no decision yet on whether to revise the WHO’s pandemic alert, now at 5. He said it could drop to 4 or rise to the top of its 6-point scale, which would activate emergency response plans to fight the virus.

“I think all these possibilities are open right now, although again it’s quite likely we could go to Phase 6 in the near future,” he said.

http://www.theglobeandmail.com/servlet/story/RTGAM.20090507.wflumain0507/BNStory/International/home


Second Strain Might Have Caused Some Severe Cases In Mexico, Investigators Say

May 7, 2009

Second Strain Might Have Caused Some Severe Cases In Mexico, Investigators Say

Via NPR

A new discovery from Canada raises the question — has a new mutation in an ordinary flu virus been causing some of the recent respiratory disease hospitalizations and deaths in Mexico?

It’s too soon to tell, but scientists in Vancouver are wondering. They’ve found two mutations in H3N2, a regular seasonal flu virus that’s been circulating in North America since last fall. (The swine flu virus is a type of H1N1.)

The mutations affect a protein called hemagglutinin that sits on the outer coat of Type A flu viruses. That’s what the “H” stands for in H1N1, H3N2 and other Type A viruses. (The “N” stands for neuraminidase, another surface protein.)

The new version of H3N2 has shown up in a number of nursing home patients in British Columbia, though not yet in the general community there. And this week the Canadian researchers spotted it when they did a complete genetic analysis of a flu virus that sickened a Canadian traveler who had just returned from Mexico.

This raises the possibility that the traveler became infected in Mexico, says Dr. Robert Brunham, chief of the British Columbia Centre for Disease Control. If so, the H3N2 virus circulating in Mexico may have the same two mutations as those being found in British Columbia patients who haven’t been to Mexico .

“In British Columbia, the H3N2 virus causes more severe cases of flu than H1N1 does,” Brunham says. “So we wonder if some of the severe cases in Mexico may have been caused by the variant H3N2 virus.”

There’s another potential implication of the Canadian finding.

Public health officials watch flu viruses closely for mutations that might make new variants of viruses less susceptible to flu vaccines. A strain called H3N2/Brisbane is one of the three components in this year’s seasonal flu vaccine — and it’s also in the vaccine now being made for next winter’s flu season.

So far the new variation of H3N2 hasn’t crossed the threshold of concern for scientists about the effectiveness of next season’s vaccine. But, “it only takes one more mutation” to cross that threshold, Brunham says.

But nobody can say yet whether the new H3N2 mutant has been circulating widely in Mexico. That’s something researchers really want to find out ASAP.

British Columbian health officials have tested a number of people who have returned from Mexico recently suffering from cold or flu symptoms, along with hundreds of non-travelers. Most didn’t have any sort of flu. Among the 10 percent who did test positive for flu, they were split 50-50 between H1N1 and H3N2 types.

However, health officials have so far only done close genetic analysis on one Mexico traveler. So they can’t say how many of the others have the new version of H3N2.

8:48 AM ET | 05-06-2009


‘Pandemic,’ not ‘Duck and Cover’

May 7, 2009

The Geopolitics of Pandemics
May 4, 2009 |

by George Friedman Stratfor

WHO level 5 Panic reaction

This panic had three elements. The first related to the global nature of this disease, given that flus spread easily and modern transportation flows mean containment is impossible. Second, there were concerns (including our own) that this flu would have a high mortality rate. And third, the panic centered on the mere fact that this disease was the flu.

News of this new strain triggered memories of the 1918-1919 flu pandemic, sparking fears that the “Spanish flu” that struck at the end of World War I would be repeated. In addition, the scare over avian flu created a sense of foreboding about influenza — a sense that a catastrophic outbreak was imminent.

By midweek, the disease was being reported around the world. It became clear that the disease was spreading, and the World Health Organization (WHO) declared a Phase 5 pandemic alert. A Phase 5 alert (the last step before a pandemic is actually, officially declared, a step that may be taken within the next couple of days) means that a global pandemic is imminent, and that the virus has proved capable of sustained human-to-human transmission and infecting geographically disparate populations. But this is not a measure of lethality, only communicability, and pandemics are not limited to the deadliest diseases.

‘Pandemic,’ not ‘Duck and Cover’

To the medical mind, the word “pandemic” denotes a disease occurring over a wide geographic area and affecting an exceptionally high proportion of the population. The term in no way addresses the underlying seriousness of the disease in the sense of its wider impact on society. The problem is that most people are not physicians. When the WHO convenes a press conference carried by every network in the world, the declaration of a level 5 pandemic connotes global calamity, even as statements from experts — and governments around the world — attempt to walk the line between calming public fears and preparing for the worst.

The reason to prepare for the worst was because this was a pandemic with an extremely unclear prognosis, and about which reliable information was in short supply.

A good analysis worth to read entirely.

Snowy Owl


WHO to Declare Level 6 Flu Pandemic

May 4, 2009

WHO to Declare Level 6 Flu Pandemic

President Barack Obama in his weekly radio address reiterated some of the administration’s recommendations, including asking schools with confirmed cases to close for up to 14 days, and urging businesses to let sick employees take all the sick days they need.

Many people in the Public Health field saw it coming since few weeks.  Yesterday Margaret Chan, director of the WHO via few selected interviews with the medias (the first since the outbreak of the 2009 H1N1).

Wall Street Journal

“There is a lot of misunderstanding in terms of fear and death,” Margaret Chan, the United Nations public health agency’s director-general, told the Wall Street Journal Sunday. “It doesn’t mean death in big numbers is going to happen.”


Once the disease begins spreading in a sustained way in other parts of the world, WHO protocols compel her to make the declaration, she told the Journal, even though the strain isn’t as deadly as most people tend to associate with the word “pandemic”.

In the Financial Times

The head of the World Health Organisation hit back at critics who have accused it of over-reaction to the swine flu crisis, warning it may return “with a vengeance” in the months ahead.

In her first extensive media interview since alerting the world to a potential flu pandemic nine days ago, Margaret Chan, the agency’s director-general, told the Financial Times that the end of the flu season in the northern hemisphere meant an initial outbreak could be milder but then a second wave more lethal, as happened in 1918.

“We hope the virus fizzles out, because if it doesn’t we are heading for a big outbreak.” But she said: “I’m not predicting the pandemic will blow up, but if I miss it and we don’t prepare, I fail. I’d rather over-prepare than not prepare.”

She stressed that a likely increase to the agency’s highest “level six” pandemic alert did not necessarily mean “every country and every individual will be affected” with many more deaths.

Rather “it is a signal to public health authorities to take appropriate measures” such as intensified disease surveillance.
http://www.ft.com/cms/s/0/e6260d9a-37d4-11de-9211-00144feabdc0.html

Then of course Market Watchers got the message

WHO reportedly prepares to declare pandemic
By Shawn Langlois, MarketWatch
Last update: 4:33 p.m. EDT May 3, 2009

http://www.ft.com/cms/s/0/e6260d9a-37d4-11de-9211-00144feabdc0.html
SAN FRANCISCO (MarketWatch) — The World Health Organization’s chief is reportedly on the brink of declaring the outbreak of a new strain of A/H1N1 swine flu a pandemic, though she said that doesn’t necessarily mean the disease is highly lethal or that it will hit the entire globe.

“There is a lot of misunderstanding in terms of fear and death,” Margaret Chan, the United Nations public health agency’s director-general, told the Wall Street Journal Sunday. “It doesn’t mean death in big numbers is going to happen.”
Once the disease begins spreading in a sustained way in other parts of the world, WHO protocols compel her to make the declaration, she told the Journal, even though the strain isn’t as deadly as most people tend to associate with the word “pandemic”.
Chan said that while the world overall is much better prepared for a pandemic than it was just a few years ago, many poor, developing countries remain particularly exposed.

In order to understand the Coherence od these measures refer to

http://www.dailykos.com/story/2009/5/2/727192/-H1N1:-Why-Do-Schools-Close,-And-When-Do-They-Open

L’OMS prête à passer au niveau 6 de son alerte at http://www.flutrackers.com/forum/showthread.php?t=102536

H1N1: Why Do Schools Close, And When Do They Open? at  http://www.flutrackers.com/forum/search.php?searchid=1233601&pp=25&page=2

“Los virus de la gripe son tramposos, no hay que confiarse” cf: http://www.elpais.com/articulo/sociedad/virus/gripe/tramposos/hay/confiarse/elpepusoc/20090504elpepisoc_3/Tes


WHO reportedly prepares to declare pandemic

May 4, 2009

WHO reportedly prepares to declare pandemic

http://www.marketwatch.com/…

SAN FRANCISCO (MarketWatch)

The World Health Organization’s chief is reportedly on the brink of declaring the outbreak of a new strain of A/H1N1 swine flu a pandemic, though she said that doesn’t necessarily mean the disease is highly lethal or that it will hit the entire globe.

“There is a lot of misunderstanding in terms of fear and death,” Margaret Chan, the United Nations public health agency’s director-general, told the Wall Street Journal Sunday.

“It doesn’t mean death in big numbers is going to happen.”

Once the disease begins spreading in a sustained way in other parts of the world, WHO protocols compel her to make the declaration, she told the Journal, even though the strain isn’t as deadly as most people tend to associate with the word “pandemic”.

snip

President Barack Obama in his weekly radio address reiterated some of the administration’s recommendations, including asking schools with confirmed cases to close for up to 14 days, and urging businesses to let sick employees take all the sick days they need.

Snowy


Non Pharmaceutical Intervention, NPI meditations

May 4, 2009

Owl Train to NPI Station

Non Pharmaceutical Interventions Station reside in a Village in Regions of North America.

In these Villages they usually have few groups;

The Free for All,

Clean-Cut Red Necks and

The Ponderers

Among those who ponder on NPI there are  the Consensuals whose

Credo is Reduce morbidity and mortality in a crisis.

What is Great in NPI Station is the Gathering of Public Health Officers with the the groups of the Village.

At the Top of the door of NPI Station is written;

“First thing First”

At the Village, the Medias welcomed Public Health Officine on spot or somewhere else mostly tributary of the ‘Mood’ of a given Region.

In the Owl Train there are always newspapers or documents left on Purpose for the Next Host.

Here it is

H1N1: Why Do Schools Close, And When Do They Open?
by DemFromCT

Sun May 03, 2009 at 08:02:03 AM PDT

CDC says its own count is outdated almost as soon as it’s announced. More cases are being confirmed daily. About one-third so far are people who had been to Mexico and probably picked up the infection there. Many newly infected people are getting the illness in the U.S., and the CDC says it probably still is spreading.

In this case, there are a lot of things that really need explaining:
what a pandemic is (based on spread, not severity)

why there are school closures with only a handful of cases

why this appears to be no worse than seasonal flu – yet isn’t seasonal flu and has to be treated differently

why testing isn’t instantly available (needs sophisticated PH lab testing)

why not everyone needs tamiflu even though tamiflu “works” (mild flu does not need treatment, regardless of seasonal or swine designation)

So let’s tackle some of those difficult points, starting with school closure.

The rationale for school closure was developed in concert with the idea that a pandemic means a widespread geographic range — for the WHO, it has got to be on two continents:

Phase 5 is characterized by human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short.

Phase 6, the pandemic phase, is characterized by community level outbreaks in at least one other country in a different WHO region in addition to the criteria defined in Phase 5. Designation of this phase will indicate that a global pandemic is under way.

For a given region, even in a pandemic, spread may have just started to get underway.

See CDC graph for the initiation, acceleration and peak:

We are not at the peak now (but we might be at the acceleration interval.) It’s early and worse things can come. So wouldn’t that mean we are at phase 6? Well, the thought all along was that it all would start in Southeast Asia and then at Phase 6, come to San Diego. Acceleration matches “spread throughout United States” on the top of the CDC graph and sits within phase 6, and with 21 states involved, we properly might now describe things as exactly that. That’s why WHO recently revised the phases. In the new method, phase 5 simply means widespread in one region. In fact, it’s in San Diego, and it will be Phase 6 when it moves to Hong Kong or New Zealand or the UK. Therefore, moving to phase 6 doesn’t affect what we already have in the US. Declaring a pandemic is for the rest of the world. We got what we got right here, right now, whatever it’s called.

The peak means sick people, and hospitalizations, and some death. It would be helpful to shrink it, delay it, and mitigate it.

The three major goals of mitigating a community-wide epidemic through NPIs [non-pharmaceutical interventions] are

1) delay the exponential increase in incident cases and shift the epidemic curve to the right in order to “buy time” for production and distribution of a well-matched pandemic strain vaccine,

2) decrease the epidemic peak, and

3) reduce the total number of incident cases and, thus, reduce morbidity and mortality in the community (Figure 1). These three major goals of epidemic mitigation may all be accomplished by focusing on the single goal of saving lives by reducing transmission. NPIs may help reduce influenza transmission by reducing contact between sick persons and uninfected persons, thereby reducing the number of infected persons. Reducing the number of persons infected will also lessen the need for healthcare services and minimize the impact of a pandemic on the economy and society.

The surge of need for medical care associated with a poorly mitigated severe pandemic can be only partially addressed by increasing capacity within hospitals and other care settings. Thus, reshaping the demand for healthcare services by using NPIs is an important component of the overall strategy for mitigating a severe pandemic.

The less severe the pandemic, the less mitigation is needed. But as far as that peak goes, here’s the goal:

Coherent, Clear,  Swift and Bold Pulic Health Message, a Must Read at

http://www.dailykos.com/story/2009/5/2/727192/-H1N1:-Why-Do-Schools-Close,-And-When-Do-They-Open

What For, Why Now and … the Parent is left with Consequences.