Thursday, April 30, 2009

US officials continue to close schools

On Thursday, the swine flu outbreak caused schools in 14 states to shut their doors on more than 160,000 schoolchildren, and additional closures could affect as many as 223,700 students in 17 states.In total, more than 100 school systems have closed at least one school as the nation tries to stifle the spread of the disease. In Texas Wednesday night, officials announced that the entire Fort Worth school system would be closed through at least May 8 as a precaution, idling 80,000 children in 140 schools.ABC News link

April 30, 2009 | Permalink | TrackBack (0)

Below is the best North American map I've seen. It is the map from the Pan-American Health Organization -- which is the WHO region for the Americas. It doesn't contain some of the Central American and South America information, but it does provide a good overview of North America  PAHO Flu Map link  To see a larger version, just click on this map.

  1. Influenza_porcina_a_(h1n1)_043009_1100h_english

April 30, 2009 | Permalink | TrackBack (0)

April 30th Information from the Pan-American Health Organization

To date, the United States has confirmed a total of 109 human cases of swine influenza A H1N1: 1 in Arizona, 14 in California, 1 in Indiana, 2 in Kansas, 2 in Massachusetts, 1 in Michigan, 1 in Nevada, 50 in New York City, 1 in Ohio, 10 in South Carolina and 26 in Texas. Other suspected cases are being investigated. 5 hospitalizations and a death have been registered. The dead case is a child of 22 months old, from Mexico who died in a hospital of Houston, Texas area.

The most recent cases detected as well as the registered death suggest that more serious cases could appear in the United States.

From 17 to 29 April, Mexico has reported 1,918 suspected cases of influenza with severe pneumonia including 84 deaths. The suspected cases were recorded in all Mexican states. Most of them in the Federal District, Guanajuato, State of Mexico, Aguascalientes, Queretaro and San Luis Potosí. The majority of these have occurred in previously healthy young adult people. There have been few cases in individuals under 3 or over 59 years old. 933 of the suspected cases are currently hospitalized.

The number of probable cases of swine influenza A H1N1 remains at 286, and a total of 97 cases has been confirmed. The considerable variation in the number of confirmed cases as of today is due to the recent laboratory confirmation of samples collected in previous weeks. The number of confirmed dead cases remains at 7. This figure is also subject to variations depending on the new laboratory information.

In Canada, to date 19 human cases of swine influenza A H1N1 have been confirmed (2 in Alberta, 4 in the province of New Scotland, 6 in British Columbia and 7 in Ontario) some of them with recent trip history to Cancun, Mexico. All the cases developed a mild form of influenza like illness. 2 of the cases presented, in addition, gastrointestinal symptoms. All of them are currently recovered and none required hospitalization. Laboratory tests were conducted in Winnipeg, Canada. `Indigenous` transmission is not discarded since not all the confirmed cases have trip history to Mexico.

The press has reported information on suspected cases in several countries of the Region; however this information has not been confirmed.

International Health Regulations (IHR)

At the request of the Director-General (DG) of WHO, the IHR Emergence Committee has been summoned and is advising the DG on the event. On its first day of deliberation, 25 April, it concluded that the present event constitutes a Public Health Emergency of International Concern.

On 29 April 2009, the DG decided to elevate the pandemic alert to Phase 5. In order to come to this urgent decision, the DG considered epidemiological information from the most affected countries, as well as the result of the scientific meeting held that same day. The latter indicated existence of sustained outbreaks of swine influenza A H1N1 at the community level in more countries within the Region.

The decision to increase the pandemic level of the alert should permit Member States to provide the required leadership and coordination as well as to consider the possibility of executing their contingency plans.

The DG recommends not closing borders or restricting travel. However, it is prudent for people who are sick to delay travel. Moreover, returning travelers who have become sick should seek medical attention in line with guidance from national authorities.

Production of seasonal vaccine should continue, but at the same time, WHO is making all the efforts to facilitate the process of development of a vaccine against swine influenza A H1N1.
The Committee will continue to advise the DG on the basis of the available information.


Enhanced surveillance

At this time, enhanced surveillance is recommended. On its Web page, PAHO has published orientations for the enhancement of surveillance activities, which are directed to the investigation of:

  • Clusters of cases of ILI/SARI of unknown cause
  • Severe respiratory disease occurring in one or more health workers
  • Changes in the epidemiology of mortality associated with ILI/SARI; increase of observed deaths by respiratory diseases; or increase of the emergence of severe respiratory disease in previously healthy adults/adolescents.
  • Persistent changes observed in the response to the treatment or evolution of a SARI.
    The following risk factors should also cause suspicion of swine influenza A H1N1 virus:
  • Close contact with a confirmed case of swine influenza A H1N1 while the case was sick.
  • Recent travel to an area where there are confirmed cases of swine influenza A H1N1 have been confirmed

Virological surveillance of swine influenza A H1NI

It is recommended that National Influenza Centers (NIC) immediately submit to the WHO Collaborating Center for influenza (CDC of the United States) all positive but unsubtypable specimens of influenza A. Shipment procedures are the same as those used by NICs for seasonal influenza specimens.

The test protocols for the detection of seasonal influenza by Polymerase Chain Reaction (PCR) cannot confirm swine influenza A H1N1 cases. The Centers for Disease Control and Prevention of the United Sates are preparing testing kits that will include the primers and probes as well as the required positive control samples. The kits will be sent in the first week of May to those NICs that currently use the CDC protocol.

Infection prevention and control in health care facilities

Since the main form of transmission of this disease is by droplets it is recommended strengthening the basic precautions to prevent their dissemination, for example the hygiene of hands, adequate triage in the health facilities, environmental controls, and the rational use of the personal protective equipment in accordance with the local regulations.

The complete guides “Epidemic-prone & pandemic-prone acute respiratory diseases Infection prevention & control in health-care facilities” are available at:

Click on the Map to enlarge



April 30, 2009 in Governance/Management | Permalink | TrackBack (0)

Reposted: Assessing Community Mitigation Efforts that Should be Implemented - Second Guessing the CDC

Original 4/26 post

I admit that there are enormous information asymetries between the CDC and me -- as well as an enormous difference in expertise.  I have been worried that CDC was moving too slowly -- perhaps because it has never dealt with a pandemic within institutional memory and perhaps because the White House is worried about the impact that pandemic precautions will have on the economic situation (assuming that this is a false alarm - and the flu does not spread or it remains milder than the Mexico strain).  The CDC's actions seem consistent with the WHO analysis that we cannot contain the international spread of the disease -- the cat is out of the bag, the horse is out of the barn -- and all we can do is mitigate and ride out whatever this disease has in store for us.

It is gratifying to see that the US supply of Tamiflu is up to 50 million courses.  That's enough to cover 15% of the population, though a tad short of the 25% goal that the federal government set.  Together with the available supplies in state and local government stores, corporate stores, and health care provider supplies, it looks like there is a good chance that there is enough Tamiflu in the US to cover any probable outbreak of swine flu.

The virulence of the flu is still a question mark.  No one has convincingly indicated why the Mexico experience is so much different.  Certainly, there appears to be rapid human-human transmission, but most cases outside Mexico have been mild.  Even so, the CDC is not placing much weight on the mild illness manifested to date in the US.  In Dr. Besser's words, the CDC expects a full spectrum of disease to occur -- meaning serious illness and some deaths in the U.S.

The death toll in Mexico is reportedly about 10%, which is vastly more virulent than the 1918 flu, which killed between 20 - 50 million people (including my paternal grandmother) and reduced global domestic product between 2.4 - 16.9%.  That flu killed roughly 2% of its victims, which were dominantly young, healthy adults  -- the Mexico flu has killed 10% of its victims, again dominantly young, healthy adults.  At that rate, we could see more than 50 million deaths with this flu if it spirals out of control.  But then again, we can't simply extrapolate from the current "kill rate" because that likely reflects the most serious illnesses, not the norm.

So  what should a responsible community in an unaffected state do at this point?  My community, for example.

To begin an analysis of what communities should be doing, start with Pandemic severity index the pandemic severity index.  Based on current data from Mexico, the case/fatality ratio appears to be Category 5.  However, based on current data (admittedly still sparse from the US), the ratio has been category 1.  It increased to category 4 with the first death, but has fallen back to category 3 as more confirmed cases occur in the US without additional deaths (4/29 and 4/30 update)  Since CDC and WHO have still not explained the difference in ratio between genetically identical viruses, one could simply split the difference and call this a category 3 pandemic.  However, since the good results in the US seem attributable to rapid treatment with effective anti-viral drugs and anti-viral supplies may not remain sufficient to treat everyone who is infected or at high risk due to close contact with infected persons, it might be prudent to treat this as a category 4 pandemic. 

While there are 50 million courses in the US stock, that only covers roughly 17% of the US population with a single treatment.  Preventative treatment for those in health care and public safety positions who are frequently exposed will consume up to 15 million of those courses, reducing treatment coverage down to about 12%.  Assuming that both US stocks and other stocks held by state and local governments, health providers, and corporations are used only to treat the seriously ill, that should be enough for the first wave.  But, the second or third waves, perhaps next fall before a vaccine is available, will be met with insufficient stores of anti-viral drugs and the virus may mutate to become resistant to the current drugs.  So, it would seem wise to depend on non-pharmaceutical approaches to reduce disease incidence and conserve treatment course.  In other words, to use community mitigation measures to increase social distancing so that we can contain the virus outbreaks without everyone getting exposed and a bunch of people needing treatment.  (4/30 update)

It is this uncertainty that has led CDC to issue interim guidance on community mitigation because previous planning had been done based on the PSI categories

The next question is when should we act?  That depends upon the WHO phase/US stage.  Note that the WHO phase has been declared at a phase 5.  The US stage should be considered a stage 5 (cases spread throughout the US). That means that all of the measures in the plan should be activated now.  I can only speculate why the WHO and US CDC are moving more slowly -- perhaps because they believe that no one can react more rapidly.  As of 4/30, it appears to me that all states, even unaffected states, are implementing their pandemic response plans.  Still a day or two late and a dollar short.

Phases stages

But, assuming a Category 3 or 4 PSI pandemic is occurring and that we are at stage 5, what should happen?  It seems to me that all of the community mitigation measures and interventions in category 4,5 should be recommended except that I would close schools for a week (and depending upon events up to 4 weeks) at this time rather than up to 12 weeks.If you click on the image below, you will be able to read the recommended measures in a separate window.


4/29 PM update

Even a day makes a difference!  WHO is now considering increasing its phase to Phase 5.  The US now has a death rate that exceeds 1%, so the Pandemic Severity Index in the US is a Category 4 severity, especially given the death rate in Mexico which appears to be in excess of 2% and thus a Category 5 severity.  So NOW would be the time to begin all of those community mitigation efforts in every affected state....and at least most of them throughout the US. 

4/30 update

It seems as though state and local governments are now acting aggressively to close schools whenever a probable case is identified.  That appears to be an adequate response.  In Oregon, state officials have suggested that closures will be for about a week -- which is enough time for exposed students to become symptomatic, seek treatment, and be diagnosed as probable cases (although not confirmed).  Response seems to be catching up to the situation.

Mitigation by pandemic severity  

April 30, 2009 in Governance/Management | Permalink | Comments (1) | TrackBack (0)

Colorado confirms 2 cases

Colorado health officials said Wednesday they were awaiting test results for what they called five suspected cases of swine flu. Thursday morning, they announced 2 cases have been confirmed. The 2 confirmed cases are in Arapahoe and Douglas counties.News link

April 30, 2009 | Permalink | TrackBack (0)

Swine Flu spreads worldwide -- at least 32 nations have suspected cases, 11 nations have 257 (+ at least 13 not yet reported) confirmed cases with 8 confirmed deaths

Swine Flu World Map

Thursday, April 30th regular AM Update

WHO Update 6 added the Netherlands to the list of countries, with one confirmed case.  The cases from Costa Rica and Peru have not yet been reported to WHO.  The additional New Zealand cases have not yet been reported to WHO.  WHO's Canadian count has jumped from 13 to 19.  WHO's UK count has increased from 5 to 8.  The total count of confirmed cases reported to WHO is now 257.

Thursday, April 30th early AM Update

There's so much to take in that the PM update has become an early AM update.

WHO has not published another update on international reported, confirmed cases. Based on news reports, confirmed cases include  Austria (1), Canada (13), Germany (3), Israel (2), New Zealand (14), Spain (10), the United Kingdom (5), Costa Rica (2) and Peru(1).  In both New Zealand and Spain, there are large numbers of suspected cases that have not yet been confirmed. 

Wednesday, April 29th AM Update

WHO has announced reported confirmed cases in 9 nations; a total of 148 reported confirmed cases; in addition to US and Mexico, confirmed cases include  Austria (1), Canada (13), Germany (3), Israel (2), New Zealand (3), Spain (4) and the United Kingdom (5). The US has reported 91 confirmed cases and 1 death, currently providing a case/fatality ratio of just over 1%.  Mexico has reported 26 confirmed cases and seven deaths.   That would be a case/fatality ratio over 25%, however, the vast bulk of Mexican cases and deaths have not yet been reported and confirmed.  Assuming the number of suspected cases (2517 with 159 suspected deaths) turn out to be accurately identified, this provides a case/fatality ratio of 6+%.  That is about 3 times as deadly as the 1918 Spanish flu pandemic, which killed 20- 40 million people.  Fortunately, we have large quantities of anti-viral drugs and have been planning for this event for several years now, so deaths should be extremely limited.

Tuesday April 28th update (PM):

According to AP, the confirmed Canadian cases now number 13, rather than six. AP report Both Spain and Israel now have 2 confirmed cases according to WHO, with WHO reporting 2 confirmed New Zealand cases and 2 confirmed UK cases, rather than the 3 NZ cases previously reported..

Denmark, Columbia, Czech Republic, Australia, and Russia have joined the list of countries with suspected cases.

Tuesday April 28th update (AM):

Israel and New Zealand have confirmed cases.  Switzerland added to suspected case list .Washington Post link  The Washington Post has a nice map, but it only tracks North American cases. WP map  The New York Times has a global map showing both confirmed and suspected cases.  NYT graphic  However, both of the maps are lagging behind -- the NYT didn't pick up the 3 confirmed New Zealand cases or the suspected cases in the EU.

Monday April 27th Update

New Zealand news link

There have been six lab-confirmed cases of mild swine flu in Canada and one in Spain, which became the first country in Europe to confirm a case after a man who returned from a trip to Mexico last week was found to have the virus. Spain has 26 suspected cases under observation and a New Zealand teacher and a dozen students who recently travelled to Mexico are being treated as likely mild cases  Countries including Australia, France, Germany, Norway, Sweden, Israel, Guatemala, Costa Rica and South Korea are all testing suspected cases of the flu. In the first confirmed cases in Britain, Scotland's health minister says two people tested positive for swine flu.

The Scottish cases bring the number of nations with confirmed cases to five and the number of nations with suspected cases to 14.

April 30, 2009 in Australia, EU, Governance/Management, International, North America, Physical Science, Science, Travel, US | Permalink | TrackBack (0)

WHO Update 6 - April 30th

Influenza A(H1N1) - update 6

30 April 2009 -- The situation continues to evolve rapidly. As of 17:00 GMT, 30 April 2009, 11 countries have officially reported 257 cases of influenza A (H1N1) infection.

The United States Government has reported 109 laboratory confirmed human cases, including one death. Mexico has reported 97 confirmed human cases of infection, including seven deaths.

The following countries have reported laboratory confirmed cases with no deaths - Austria (1), Canada (19), Germany (3), Israel (2), Netherlands (1), New Zealand (3), Spain (13), Switzerland (1) and the United Kingdom (8).

April 30, 2009 in Governance/Management | Permalink | TrackBack (0)

CDC Swine Flu Report - April 30th: South Carolina added to list of states with confirmed cases (10 cases) and Texas also adds 10 more cases

Swine Influenza (Flu)

Swine Flu website last updated April 30, 2009, 10:30 AM ET

U.S. Human Cases of Swine Flu Infection
(As of April 30, 2009, 10:30 AM ET)
# of laboratory confirmed cases
Arizona 1  
California 14  
Indiana 1  
Kansas 2  
Massachusetts 2  
Michigan 1  
Nevada 1  
New York 50  
Ohio 1  
South Carolina
TOTAL COUNTS 109 cases 1 death
International Human Cases of Swine Flu Infection
See: World Health OrganizationExternal Web Site Policy.

In response to an intensifying outbreak in the United States and internationally caused by a new influenza virus of swine origin, the World Health Organization raised the worldwide pandemic alert level to Phase 5External Web Site Policy. on April 29, 2009. A Phase 5 alert 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.”

The United States Government has declared a public health emergency in the United States. CDC’s response goals are to reduce transmission and illness severity, and provide information to help health care providers, public health officials and the public address the challenges posed by this emergency. CDC is issuing and updating interim guidance daily in response to the rapidly evolving situation. CDC’s Division of the Strategic National Stockpile (SNS) continues to send antiviral drugs, personal protective equipment, and respiratory protection devices to all 50 states and U.S. territories to help them respond to the outbreak. The swine influenza A (H1N1) virus is susceptible to the prescription antiviral drugs oseltamivir and zanamivir. In addition, the Federal Government and manufacturers have begun the process of developing a vaccine against this new virus.

April 30, 2009 in Governance/Management | Permalink | TrackBack (0)

Mexico to take 5 day break at home to stop spread of swine flu -- but ever optimistic Americans are going about business as usual

The NY Times reported this morning:

As the swine flu virus appeared in new locations as far apart as Peru and Switzerland on Thursday, Mexicans braced for a national shutdown of offices, restaurants, schools and even the stands of soccer stadiums in an attempt to slow the spread of the disease. In nationally televised speech on Wednesday night, the Mexican president, Felipe Calderón, said that many public services would be closed Friday through Tuesday, encompassing a long holiday weekend. Most government offices and many private businesses will be ordered closed, restaurants, schools and museums will remain shuttered, and spectators will be barred from all professional soccer matches. Churches are expected to be nearly empty on Sunday. Mexico, the epicenter of the disease, Mr. Calderón urged much broader precautions [than those being taken in Britain]. People should stay inside their homes during the holiday hiatus, he said, and the shutdown and restrictions could possibly be extended further into next week.  The Mexican minister of health, Jose Cordova, said all nonessential federal services will shut down, and Mexico City extended the federal ban to include health clubs, gyms, museums and movie theaters.Police stations, airports, bus stations and the capital’s subway system were to remain open under the federal plan, along with banks, food stores, pharmacies and gasoline stations.

Some 2,500 Mexicans have been sickened since the swine flu outbreak began last week in the town of La Gloria, 110 miles east of Mexico City. Mexico has reported just 99 confirmed cases of swine flu to the W.H.O., along with eight deaths, although as many as 168 people are suspected to have died from the disease there.

Contrast this reaction with that of NYC:

The number of swine flu cases in New York City continues to grow, with hundreds of confirmed or suspected cases mostly among students. Four schools - two in Brooklyn and two in Queens - will be closed for the rest of the week to prevent any further spread of this new variant of influenza. But with only one reported death and few reports of severe illness in the U.S. attributed to swine flu, New Yorkers are mostly brushing off worries about the illness. 

Anna Garcia and daughter
Anna Garcia and daughter
The number of swine flu cases has been growing, but New York seems more like a city under the spell of spring weather rather than worried about a possible pandemic. Parents, students and workers say they're watchful, but not alarmed. Letia Frandino is from the borough of Queens, where the New York outbreak was first detected, says this is the reason why she paid closer attention to the alert: "... because it was in Queens. I have heard that we shouldn't be panicking because there are still mild cases so far in the United States, so that's what we are going on," she said.  Anna Garcia, picking up her daughter after school, said she's also not worried. "I'm a public school teacher in Brooklyn, in a community that's mostly from Mexico, and they don't seem to be panicking. And as long as you keep your hands clean," she says, "you tell the children to keep, you know, like you would any cold or flu, you're just telling them to protect themselves."  Students doing homework at a park in Manhattan said they've been warned at school about what could happen if swine flu emerges there. One student, Alison, says, "They were saying how all the kids would miss school for two days while they cleaned the whole school, and the kids would have to go to doctors." Student Jonathan adds, "No one really wears masks, like they're not afraid, it's just the flu. But they don't know how bad it is, maybe?"

Michael Bloomberg
Michael Bloomberg
On Tuesday, New York Mayor Michael Bloomberg said swine flu is expected to spread around the city - as some form of influenza does each year - but that, for now, it does not look as if it will cause more deaths than other flus.  "From what we know now, swine flu seems to spread similarly to seasonal garden-variety flu, that we regularly see in our city and we have no reason at the moment from what we have seen here to believe its symptoms are any more severe," he said.  The mayor said that people with flu should stay home, but that no one in New York has yet become seriously ill. 

"Almost every case has been very mild," Bloomberg said. "And the process of going from catching it to noticeably getting better, has been in a few days, very quick."  That may be why New Yorkers don't appear worried, and subway cars are as jammed as ever, with few people wearing masks.  "What can you do?" one man said. "You have to get around. Wash your hands, just be careful what you do."

The difference in New York City and Mexico City is not a difference in the virus.  It is a difference in the length of time that the virus has been active and a difference in the level of government response.  Time will tell which response is more appropriate -- but I'd prefer that the government follow the precautionary principle and err on the side of caution.  The federal government seems to be doing that, but most of the decisions about community mitigation measures are in the hands of the state and local governments, not the federal government.  With uneven response, the likelihood that everyone in the United States will get an opportunity to be exposed to this flu is high.

April 30, 2009 in Governance/Management | Permalink | TrackBack (0)

Wednesday, April 29, 2009

HHS Video on Swine Flu

April 29, 2009 in Physical Science | Permalink | TrackBack (0)

WHO raises alert level to Phase 5 - there will be a pandemic.

WHO link to Video of press conference

Press conference video file for direct downloading

There will be a pandemic -- the question is

how severe?  Dr. Chan says WHO is now

mobilizing every resource - financial

resources from donor countries and the World

Bank, vaccine and drug manufacturers,

governments - in order to ramp up

preparedness and response.  The time to act

is now.

The WHO Statement:

Statement by WHO Director-General, Dr Margaret Chan
29 April 2009

Swine influenza

Ladies and gentlemen,

Based on assessment of all available information, and following several expert consultations, I have decided to raise the current level of influenza pandemic alert from phase 4 to phase 5.

Influenza pandemics must be taken seriously precisely because of their capacity to spread rapidly to every country in the world.

On the positive side, the world is better prepared for an influenza pandemic than at any time in history.

Preparedness measures undertaken because of the threat from H5N1 avian influenza were an investment, and we are now benefitting from this investment.

For the first time in history, we can track the evolution of a pandemic in real-time.

I thank countries who are making the results of their investigations publicly available. This helps us understand the disease.

I am impressed by the work being done by affected countries as they deal with the current outbreaks.

I also want to thank the governments of the USA and Canada for their support to WHO, and to Mexico.

Let me remind you. New diseases are, by definition, poorly understood. Influenza viruses are notorious for their rapid mutation and unpredictable behaviour.

WHO and health authorities in affected countries will not have all the answers immediately, but we will get them.

WHO will be tracking the pandemic at the epidemiological, clinical, and virological levels.

The results of these ongoing assessments will be issued as public health advice, and made publicly available.

All countries should immediately activate their pandemic preparedness plans. Countries should remain on high alert for unusual outbreaks of influenza-like illness and severe pneumonia.

At this stage, effective and essential measures include heightened surveillance, early detection and treatment of cases, and infection control in all health facilities.

This change to a higher phase of alert is a signal to governments, to ministries of health and other ministries, to the pharmaceutical industry and the business community that certain actions should now be undertaken with increased urgency, and at an accelerated pace.

I have reached out to donor countries, to UNITAID, to the GAVI Alliance, the World Bank and others to mobilize resources.

I have reached out to companies manufacturing antiviral drugs to assess capacity and all options for ramping up production.

I have also reached out to influenza vaccine manufacturers that can contribute to the production of a pandemic vaccine.

The biggest question, right now, is this: how severe will the pandemic be, especially now at the start?

It is possible that the full clinical spectrum of this disease goes from mild illness to severe disease. We need to continue to monitor the evolution of the situation to get the specific information and data we need to answer this question.

From past experience, we also know that influenza may cause mild disease in affluent countries, but more severe disease, with higher mortality, in developing countries.

No matter what the situation is, the international community should treat this as a window of opportunity to ramp up preparedness and response.

Above all, this is an opportunity for global solidarity as we look for responses and solutions that benefit all countries, all of humanity. After all, it really is all of humanity that is under threat during a pandemic.

As I have said, we do not have all the answers right now, but we will get them.

Thank you.

April 29, 2009 in Governance/Management | Permalink | Comments (0) | TrackBack (0)

Swine Flu Sells

I haven't tried to find out other blog and website traffic figures, but based on my figures, swine flu "sells."  This might be a good time to remind readers that all royalties from this blog go to fund water and sanitation projects in developing countries, not my extravagant lifestyle!Swine flu blogging The traffic since Sunday has exceeded the highest traffic since I began the blog three years ago.  Yet only about half of the traffic overall involves swine flu.

April 29, 2009 in Economics | Permalink | TrackBack (0)

Six Month Contraction of Economy Greater than any Prior Six Months during Post WWII Recession

I saw the news from the Commerce Department today that the US economy contracted at a 6.1% annual rate during the first quarter of this year following a 6.3% loss in GDP during the fourth quarter of 2008.  A quick glance at the CRS report on recessions indicates that no post WWII recession had two quarters of consecutive reductions in GDP in the 6+% range.  This is a much steeper recession than anything in the past. 

April 29, 2009 in Economics | Permalink | Comments (0) | TrackBack (0)

AAAS Policy Alert

For those of you who try to stay current on science policy, I am a member of AAAS and receive its policy alerts. I encourage all of you to join and subscribe to Science.  Here is today's policy alert:

AAAS Policy Alert -- April 29, 2009 

President Addresses National Academies

President Obama addressed the Annual Meeting of the National Academy of Sciences on April 27 and called for a renewed commitment to basic scientific research and education. During his speech he stated that his goal would be to increase our nation's share of federal investment in research and development (R&D) to 3 percent of gross domestic product (GDP). In recent years, the share has hovered around 2.6 percent of GDP. Furthermore, Obama announced the membership of the President's Council of Advisors for Science and Technology (PCAST). Members include past AAAS President Shirley Ann Jackson of RPI, as well as former Board member Rosina Bierbaum and current AAAS Treasurer David Shaw. They join former AAAS President John Holdren who is both the U.S. President's science advisor and co-chair of PCAST.

Budget News

The House and Senate have nominated the conferees to resolve the differences between their respective versions of the FY 2010 budget resolution. House members include: Budget Committee Chairman John Spratt (D-SC), Ranking Member Paul Ryan (R-WI), and Reps. Allen Boyd (D-FL), Rosa DeLauro (D-CT) and Jeb Hensarling (R-TX). Senate members include Budget Committee Chair Kent Conrad (D-ND), Ranking Member Judd Gregg (R-NH) and Sen. Patty Murray (D-WA). The conferees met today (April 27) to begin deliberating over a consensus document.

Other Congressional News

Congressional Climate Change Update. The House Energy and Commerce Committee held four days of hearings on the American Clean Energy and Security Act, with much debate on the merits of moving ahead on the climate and energy package. Subcommittee markup of the bill has been pushed back to next week, with details such as how to allocate permits to emit greenhouse gases and how the revenues will be used yet to be determined. Meanwhile Senate Environment and Public Works Chairwoman Barbara Boxer (D-CA) announced the formation of five working groups to find compromises in several areas of concern: regional issues, cost containment, targets and timetables, market oversight and coal research and technology. The Senate Foreign Relations Committee heard from Todd Stern, special envoy for climate change at the State Department, who testified on the diplomatic cost of inaction on climate change and emphasized the need for all countries - developed and developing - to engage in negotiations with "common but differentiated responsibilities." Stern is leading the first session of the Major Economies Forum on Energy and Climate on April 27-28, a White House initiative to develop a dialogue among major developed and developing economies on climate change.

New Bill Promotes Science Envoys. Last week, Senator Richard Lugar (R-IN) introduced legislation (S. 838) that recognizes the importance of international scientific cooperation and the work of organizations such as AAAS and the National Academies in this area. The legislation tasks the State Department to appoint Science Envoys to represent our nation and promote international collaboration.

Executive Branch

Presidential Memo on Scientific Integrity. OSTP issued a Presidential Memo on scientific integrity in the April 23 Federal Register and requests public comments on six principles for maintaining and protecting the responsible use of science in decision-making. The memo builds upon a March 9, 2009 memorandum from the President that called on OSTP to issue a set of recommendations within 120 days. OSTP has launched a blog on the subject and is seeking comments on the selection of scientists to serve in the executive branch, peer-review of science used in policy-making, access to scientific data used in policy-making, and whistleblower protection. Comments are due May 13, 2009.

NIH Stem Cell Guidelines Now Open for Comment. The NIH Guidelines for Human Stem Cell Research are now open for public comment until May 26.

NCI Director Speaks on Cancer Plan. National Cancer Institute Director John Niederhuber recently spoke of his institute's plans in the wake of President Obama's cited goal of doubling funds for cancer research. Included would be a boost in the NCI payline to fund more meritorious research grants, as well as more grants to first-time investigators and new faculty researchers. There will also be a focus on personalized cancer care.

EPA Examines Ocean Acidification. On April 14, EPA issued a Federal Register notice requesting information on ocean acidification, the changing of ocean chemistry from increases in carbon dioxide that affects coral reefs and other marine organisms. In response to a lawsuit by the Center for Biological Diversity, EPA is trying to determine whether changes are needed to the water quality criteria under the Clean Water Act. Comments are due June 15, 2009.

Toxics Reporting Tightened. As mandated in the 2009 omnibus appropriations bill, EPA finalized changes to reporting requirements under the Toxics Release Inventory that will take effect July 1. The final rules restore more stringent reporting requirements than those from a Bush-era rule that raised the pollution threshold for reporting. In 2006, AAAS submitted comments stating that the increased threshold would "threaten the ability of researchers to identify and understand potential threats to the environment and public health in a scientifically rigorous manner."

FDA Widens Access to "Morning-After" Pill. The Food and Drug Administration will now allow 17-year-olds to purchase the Plan B "morning-after" pill without a prescription, following a recent federal court order that it do so. The decision has been labeled a "triumph of science over politics" because of widespread concern that the previous administration overruled scientific advice on making the pill available over the counter, leading the FDA's top women's health official, Susan Wood, to resign in protest in 2005.

Nation's First CTO: Clarification. Last week's Policy Alert reported on the President's selection of Aneesh Chopra to be the nation's first chief technology officer. It has since been reported that the CTO will also be one of the associate directors of the Office of Science and Technology Policy (OSTP) concerned with overall technology policy and innovation strategies across federal departments. Chopra's position (which is subject to Senate confirmation) should not be confused with that of Vivek Kundra, recently named Chief Information Officer, who is located in the Office of Management and Budget (OMB), overseeing day-to-day information technology spending and interagency operations.


Climate Risk Report Released. Led by the Heinz Center and CERES, a coalition of insurance, government, environmental, and investment organizations released a report, Resilient Coasts: A Blueprint for Action that listed steps the nation can take to drastically reduce rising coastal hazard risks and their associated economic impacts.

Texas School Board Chairman Up for Confirmation. Texas State Board of Education Chairman Don McLeroy, a vocal opponent of teaching evolution, is up for Senate confirmation by the state Senate, and during a recent hearing some members of the Senate Nominations Committee expressed dissatisfaction with McLeroy's performance. One state senator said McLeroy has "created a hornet's nest" and noted that 15 bills filed during this legislative session would strip powers from the state school board. Even if McLeroy is not confirmed as chairman, he will still remain a member of the board. In other news, the Institute for Creation Research is now suing in U.S. District Court over the Texas Higher Education Coordinating Board's decision to deny its request to offer a master's degree in science education.

Animal Rights Activists Charged. Two animal rights activists have been arraigned on charges of conspiracy, stalking and other crimes, including attempted fire-bombing, against UCLA scientists engaged in animal research.

Publisher: Alan I. Leshner
Editor: Joanne Carney
Contributors: Erin Heath, Earl Lane, Steve Nelson, Al Teich, Kasey White

NOTE: The AAAS Policy Alert is a newsletter provided to AAAS Members to inform them of developments in science and technology policy that may be of interest.  Information in the Policy Alert is gathered from published news reports, unpublished documents, and personal communications.  Although the information contained in this newsletter is regarded as reliable, it is provided only for the convenience and  private use of our members.  Comments and suggestions regarding the Policy Alert are welcome.  Please write to [email protected].

April 29, 2009 in Climate Change, Energy, Governance/Management, Legislation, Physical Science, Science, Social Science, Sustainability, Toxic and Hazardous Substances, US, Water Resources | Permalink | TrackBack (0)

How this virus developed and why it may be a killer

The Mexican swine flu virus is a swine influenza A/H1N1 virus hybridized (mixed) with human and bird viruses.  We have some immunity to human flu and to some strains of swine influenza A/H1N1;  We don't have immunity to bird flu, which is why that virus is so virulent - with a kill ratio of almost 50% -- and why so much pandemic planning and preparedness focused on bird flu.

New Scientist reports:

This type of virus emerged in the US in 1998 and has since become endemic on hog farms across North America. Equipped with a suite of pig, bird and human genes, it was also evolving rapidly.  Flu infects many animals, including waterfowl, pigs and humans. Birds and people rarely catch flu viruses adapted to another host, but they can pass flu to pigs, which also have their own strains.If a pig catches two kinds of flu at once it can act as a mixing vessel, and hybrids can emerge with genes from both viruses. This is what happened in the US in 1998. Until then, American pigs had regular winter flu, much like people, caused by a mutated virus from the great human pandemic of 1918, which killed pigs as well as at least 50 million people worldwide. This virus was a member of the H1N1 family - with H and N being the virus's surface proteins haemagglutinin and neuraminidase.  Over decades, H1N1 evolved in pigs into a mild, purely swine flu, and became genetically fairly stable. In 1976, there was an outbreak of swine H1N1 in people at a military camp [Fort Dix] in New Jersey, with one death. The virus did not spread efficiently, though, and soon fizzled out.

But in 1998, says Richard Webby of St Jude's Children's Research Hospital in Memphis, Tennessee, swine H1N1 hybridised with human and bird viruses, resulting in "triple reassortants" that surfaced in Minnesota, Iowa and Texas. The viruses initially had human surface proteins and swine internal proteins, with the exception of three genes that make RNA polymerase, the crucial enzyme the virus uses to replicate in its host. Two were from bird flu and one from human flu. Researchers believe that the bird polymerase allows the virus to replicate faster than those with the human or swine versions, making it more virulent.

By 1999, these viruses comprised the dominant flu strain in North American pigs and, unlike the swine virus they replaced, they were actively evolving. There are many versions with different pig or human surface proteins, including one, like the Mexican flu spreading now, with H1 and N1 from the original swine virus. All these viruses still contained the same "cassette" of internal genes, including the avian and human polymerase genes, reports Amy Vincent of the US Department of Agriculture (USDA) in Ames, Iowa (Advances in Virus Research, vol 72, p 127). "They are why the swine versions of this virus easily outcompete those that don't have them," says Webby.

But the viruses have been actively switching surface proteins to evade the pigs' immunity. There are now so many kinds of pig flu that it is no longer seasonal. One in five US pig producers actually makes their own vaccines, says Vincent, as the vaccine industry cannot keep up with the changes. This rapid evolution posed the "potential for pandemic influenza emergence in North America", Vincent said last year. Webby, too, warned in 2004 that pigs in the US are "an increasingly important reservoir of viruses with human pandemic potential". One in five US pig workers has been found to have antibodies to swine flu, showing they have been infected, but most people have no immunity to these viruses.

The virus's rapid evolution created the potential for a pandemic to emerge in North America.  Our immune response to flu, which makes the difference between mild and potentially lethal disease, is mainly to the H surface protein. The Mexican virus carries the swine version, so the antibodies we carry to human H1N1 viruses will not recognise it. That's why the CDC warned last year that swine H1N1 would "represent a pandemic threat" if it started circulating in humans. The avian polymerase genes are especially worrying, as similar genes are what make H5N1 bird flu lethal in mammals and what made the 1918 human pandemic virus so lethal in people. "We can't yet tell what impact they will have on pathogenicity in humans," says Webby. It appears the threat has now resulted in the Mexican flu. "The triple reassortant in pigs seems to be the precursor," Robert Webster, also at St Jude's, told New Scientist.

While researchers focused on livestock problems could see the threat developing, it is not one that medical researchers focused on human flu viruses seemed to have been aware of. "It was confusing when we looked up the gene sequences in the database," says Wendy Barclay of Imperial College London, who has been studying swine flu from the recent US cases. "The polymerase gene sequences are bird and human, yet they were reported in viruses from pigs."

So where did the Mexican virus originate? The Veratect Corporation based in Kirkland, Washington, monitors world press and government reports to provide early disease warnings for clients, including the CDC. Their first inkling of the disease was a 2 April report of a surge in respiratory disease in a town called La Gloria, east of Mexico City, which resulted in the deaths of three young children. Only on 16 April - after Easter week, when millions of Mexicans travel to visit relatives - reports surfaced elsewhere in the country.

Local reports in La Gloria blamed pig farms in nearby Perote owned by Granjas Carroll, a subsidiary of US hog giant Smithfield Foods. The farms produce nearly a million pigs a year. Smithfield Foods, in a statement, insists there are "no clinical signs or symptoms" of swine flu in its pigs or workers in Mexico. That is unsurprising, as the company says it "routinely administers influenza virus vaccination to swine herds and conducts monthly tests for the presence of swine influenza." The company would not tell New Scientist any more about recent tests. USDA researchers say that while vaccination keeps pigs from getting sick, it does not block infection or shedding of the virus.

All the evidence suggests that swine flu was a disaster waiting to happen. But it got little research attention, perhaps because it caused mild infections in people which didn't spread. Now one swine flu virus has stopped being so well-behaved.

This leads us to the policy question: why should humans keep pigs?  Like other meat, pigs consume an extraordinary amount of resources to provide nutrition.  Maybe the ancient Israelites had an insight that we have lacked -- there may be more wisdom in the Torah and its laws than we knew.  Perhaps it is time, or past time, for our eating habits to evolve lest an even more virulent strain of swine flu develop.  Assuming that this pandemic passes without too many deaths, we may need to rethink whether it is good to keep large quantities of pigs.  For now, the virulent bird flu does not seem easily communicable.  Let's keep it that way. 

April 29, 2009 in Agriculture, Asia, Australia, Biodiversity, Current Affairs, Economics, EU, Food and Drink, Governance/Management, International, North America, Religion, Sustainability, US | Permalink | TrackBack (0)

WHO Update 5 - April 29th

29 April 2009 -- The situation continues to evolve rapidly. As of 18:00 GMT, 29 April 2009, nine countries have officially reported 148 cases of swine influenza A/H1N1 infection. The United States Government has reported 91 laboratory confirmed human cases, with one death. Mexico has reported 26 confirmed human cases of infection including seven deaths.

The following countries have reported laboratory confirmed cases with no deaths - Austria (1), Canada (13), Germany (3), Israel (2), New Zealand (3), Spain (4) and the United Kingdom (5).

April 29, 2009 in Governance/Management | Permalink | TrackBack (0)

CDC US information

Swine Influenza (Flu)

Swine Flu website last updated April 29, 11:00 AM ET

U.S. Human Cases of Swine Flu Infection
(As of April 29, 2009, 11:00 AM ET)
# of laboratory confirmed cases







New York City


91 cases
1 death
International Human Cases of Swine Flu Infection
See: World Health OrganizationExternal Web Site Policy.

The outbreak of disease in people caused by a new influenza virus of swine origin continues to grow in the United States and internationally. Today, CDC reports additional confirmed human infections, hospitalizations and the nation’s first fatality from this outbreak. The more recent illnesses and the reported death suggest that a pattern of more severe illness associated with this virus may be emerging in the U.S. Most people will not have immunity to this new virus and, as it continues to spread, more cases, more hospitalizations and more deaths are expected in the coming days and weeks.

CDC has implemented its emergency response. The agency’s goals are to reduce transmission and illness severity, and provide information to help health care providers, public health officials and the public address the challenges posed by the new virus. Yesterday, CDC issued new interim guidance for clinicians on how to care for children and pregnant women who may be infected with this virus. Young children and pregnant women are two groups of people who are at high risk of serious complications from seasonal influenza. In addition, CDC’s Division of the Strategic National Stockpile (SNS) continues to send antiviral drugs, personal protective equipment, and respiratory protection devices to all 50 states and U.S. territories to help them respond to the outbreak. The swine influenza A (H1N1) virus is susceptible to the prescription antiviral drugs oseltamivir and zanamivir. This is a rapidly evolving situation and CDC will provide updated guidance and new information as it becomes available.

April 29, 2009 | Permalink | TrackBack (0)

Its time to undertake all of the community mitigation efforts: we have a PSI category 4 pandemic at least and WHO is set to declare the pandemic to be stage 5

Even a day makes a difference!  WHO is now considering increasing its phase to Phase 5.  The US now has a death rate that exceeds 1%, so the Pandemic Severity Index in the US is a Category 4 severity, especially given the death rate in Mexico which appears to be in excess of 2% and thus a Category 5 severity.  So NOW would be the time to begin all of those community mitigation efforts in every affected state....and at least most of them throughout the US.  For the details about what we should do and why, see this reposting from yesterday.  Secondguessing the CDC  But suffice it to say, we need to isolate the ill, quarentine those in close contact with them at home, close schools and deliver instruction on line, reduce business meetings and encourage telework, cancel large gatherings, and in general promote social distancing.  My guess is that it will take another dozen deaths and the spread to another 15 states before the CDC issues these recommendations.   

April 29, 2009 in Governance/Management | Permalink | Comments (0) | TrackBack (0)

CDC count at 91; new confirmed cases in Michigan Massachusetts, Arizona, and Nevada; one toddler dies in Texas

Wednesday, April 29th AM update

The WSJ has a great map -- it appears to be using official CDC and WHO numbers as opposed to state and national numbers, but still its very useful.  WSJ map

We now have confirmed cases in Michigan, Massachusetts, Arizona, and Nevada and a total of 91 confirmed cases.  

The first confirmed death was a toddler who crossed the border with his family from Mexico into south Texas and who died from the new strain of swine flu in a Houston hospital. The boy, almost 2 years old, was initially treated for flu symptoms in Brownsville, at the far southern tip of Texas, and was transferred to Houston because of the severity of his systems.  The boy appears to have been vulnerable due to underlying medical conditions.  WSJ story

Tuesday, April 28th PM update

With a confirmed case in Indiana and 15 confirmed cases in California, the US case count is now 71.  ABC news link There are also suspected cases in Florida and New to NJ cases  

Richard Besser, acting director of the federal Centers for Disease Control and Prevention, declined to comment on the California investigation, but said, "I fully expect we will see deaths from this infection." ABC news link

Monday, April 27th

With three cases in Sacramento as of Monday evening, the California case count has risen to 13.  Sacramento news link  While CDC still has a total of 40 confirmed cases posted on its site, the number of confirmed cases appears to have risen to 55: 13 in California and 42 in other states.  The Sacramento cases are particularly important because they are the first in Northern California.  Texas also confirmed four more cases, bringing the state total to six.  The new cases in Dallas involve a wider age group -- a 24 year old, a 7 year old and a 3 month old.  Texas news link

April 29, 2009 | Permalink | TrackBack (0)

Tuesday, April 28, 2009

Check out Peter Gleick's blog on water issues

Gleick Joins the Blogosphere


Read and discuss everything water with internationally renowned expert Peter Gleick, president of the Pacific Institute, on his new blog.

GleickFeatured on City Brights, San Francisco Chronicle's luminary blogger site, Gleick explores the water challenges facing California, the West, and our world. Follow along as he discusses the threats to our freshwater resources and viable solutions to those threats, drawing from not only his experiences and viewpoint, but also by way of numbers: each post will include an important, unusual, or newsworthy "water number" that will highlight some piece of the water issue.

Click to check it out or join the conversation:

April 28, 2009 in International, Physical Science, US, Water Quality, Water Resources, Weblogs | Permalink | TrackBack (0)