swine flu
sporte | April 28, 2009Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn.
Activity 1. What kinds of animals get the flu?
For the past few years we've been worrying about avian (bird). Now, we're hearing about swine (pig) flu.
All of this news might you wonder just who gets the flu besides pigs, birds, and humans. We can find out by looking at the data.
Over the past few years, researchers have been sequencing influenza genomes and depositing those genomes in public databases…
revere | April 28, 2009It would be nice to think that the 28 cases at the NY Prep School are it for the city and that the virus has been contained there. But that was always more a wish than a plausible reality:
CBS 2 HD has learned of a confirmed case of swine flu at the Ernst & Young headquarters in Times Square.
One of the staffers became ill over the weekend after coming into contact with a family member who had been exposed to the virus.
The staffer is said to be resting at home and the company believes, due to the virus' 24-hour incubation period, that no one else at Ernst & Young was exposed. The…
palmd | April 28, 2009We have a lot to cover today, but first things first: the Big Question. If you'll cast your memory way back (thanks, Van) you'll remember that a good question to ask altmed followers is the one of abandonment: what would it take for them to abandon a modality? Well, the answers are in, and the one's who answered just didn't get it. For example:
[T]he question was: "Can you please give specific examples of alternative medicine theories and modalities that have been abandoned because they have been found to be ineffective?"
The short and honest answer to this is no-- I cant. But my reason…
ddobbs | April 28, 2009The excellent blog H5N1 (now covering H1N1 as well, and all over it), points us to the New York Times for an op-ed by John M. Barry, author of the definitive history of the Spanish flu in the US: Where Will the Swine Flu Go Next? Excerpt:
As the swine flu threatens to become the next pandemic, the biggest questions are whether its transmission from human to human will be sustained and, if so, how virulent it might become.
But even if this virus were to peter out soon, there is a strong possibility it would only go underground, quietly continuing to infect some people while becoming…
revere | April 27, 2009Now that the initial rush is over, time to settle in for the long(er) haul. It's 3 am here. Good time to clear the air and lighten up:
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ddobbs | April 27, 2009I'm guessing most everyone interested in swine flu already reads Effect Measure (as well you should; it was an invaluable resource in my reporting for my Slate piece on the mystery of the virulence of the outbreak in Mexico). But in case you haven't or are not, today's primer there on case fatality rates, virulence, and mortality would make an excellent start.
One of the things we'd like to know about the swine flu virus is its Case Fatality Ratio (CFR, commonly called a case fatality rate, although it isn't technically a rate but a proportion). But what is a CFR? And how is it different…
revere | April 27, 2009One of the things we'd like to know about the swine flu virus is its Case Fatality Ratio (CFR, commonly called a case fatality rate, although it isn't technically a rate but a proportion). But what is a CFR? And how is it different from a mortality rate?
The CFR is an estimate of the probability that someone with the swine flu will die of it (technically, before dying from something else or recovering). The higher the CFR, the more virulent the virus. So what's virulence? Virulence refers to the severity of the disease the virus produces. Rabies is a virulent virus. Everybody dies from it…
amillikan | April 27, 2009
Correction appended: This post incorrectly stated the Center for Disease Control as the organization responsible for raising the pandemic threat level. This is the duty of the World Health Organization.
Swine flu outbreaks are raising alarm across the globe and prompting the World Health Organizationto consider raising the pandemic threat level. For the most current interpretations of what's happening from experts on the ScienceBlogs network, see the following category threads: "Pandemic-Preparedness" and "Swine Flu" from Revere at Effect Measure, and "Influenza" and "Outbreak" from Tara…
palmd | April 27, 2009I tuned into a CDC conference call this afternoon. It was interesting. As is often the case with emerging diseases, what we don't know vastly outweighs what we do. For the best public health information in the blogosphere, and the best flu updates, go to Effect Measure.
The CDC emphasized that it's quite early and things are changing by the hour. So far 40 cases have been identified in the U.S., all of them mild, with one requiring hospitalization because of underlying medical problems. It is assumed that many more cases will be identified, and it would be unusual if at least some were not…
ddobbs | April 27, 2009
"Swine Flu and the Mexico Mystery," my story on the swine-flu outbreak, is up at Slate. It looks at a question hotly pursued right now: Why does this flu seem to take a much deadlier course in Mexico than elsewhere so far? The answers will suggest much about what's to come.
Of the two two qualities vital to a nasty pandemicm-- to spread readily, and to be deadly, -- this flu,a brand-new strain of swine flu, or H1N1, seems to possess the first: Evidence is high that it spreads readily among humans. In that sense, it's an inversion of the bird flu. Bird flu terrifies infectious disease…
revere | April 27, 2009The daily CDC conference call was not particularly informative, but these daily briefings are still extremely valuable. Things are happening fairly fast but nothing we didn't expect. There are now 40 confirmed US cases in the same 5 states (California, NY, Texas, Kansas, Ohio). The 28 new cases sere contributed by the New York prep school that had the state's first 8 cases. These additional ones are the result of continued case finding. Acting CDC Director said that the only laboratory confirmed human to human transmission is in the Kansas husband and wife (he had just returned from Mexico…
revere | April 27, 2009Usually "What did you expect?" is a rhetorical question, but we have a more serious point to make. Let's start with the familiar and move on to the less familiar. Many of you are coming here to find the latest news about swine flu. It's an imprecise term that covers two different things: what has happened that is new, in the sense of surprising and we didn't already know it would happen; and what is the current situation. Overnight (in the US) Europe (Spain) registered its first confirmed case. That's additional data but not surprising. We know this virus is seeded out there and we shouldn't…
sciencepunk | April 26, 2009
Thanks to Sandy for letting me know about the Center for Disease Control's Twitter Feed, which will keep you up to date with the current swine flu outbreak. Latest news is 20 confirmed cases in the US, with one hospitalisation, and clear human-to-human spread. Over at Effect Measure, Paul Revere has a well-informed running commentary of the emerging virus.
palmd | April 26, 2009With all the news abuzz about swine flu, it's important to remember a few things. Influenza can be very, very dangerous, but it's still just a virus, and one that we know quite well. There have been a number of flu pandemics in the last century, the most famous (and most deadly) being the "Spanish flu" of 1918-1919. That pandemic was a perfect storm. Soldiers moved back and forth between Europe and the U.S., and military bases in the U.S. weren't much better than the Western Front. Soldiers on U.S. bases lived in crowded, cold, wet conditions, and the flu moved through them rapidly,…
revere | April 26, 2009The White House briefing today had Obama written all over it. It's themes were Obama, it's tone of quiet, serious confidence were Obama. The sense of total command of the situation was Obama. There was the Obama-ese call for "personal responsibility." Government can't do everything. There are things we each have to take personal responsibility for.
Fine. I don't disagree. But I think there are some things missing from this frame. One is that it isn't a binary choice, government or the individual. We all live in a set of overlapping communities: work, home, neighborhood, civic organizations,…
palmd | April 26, 2009So far, it looks like the US Gov't is on top of this one. If you're interested in following along with the story, I strongly suggest following the Effect Measure blog. The writers know their stuff, and so far, government websites aren't all that much health.
Some basics:
As you remember, the flu virus changes over time due to "antigenic drift" and we need to make new vaccines every year. Sometimes, often due to multiple strains co-infecting the same animal, the influenza genome undergoes a more dramatic change called "antigenic shift". Influenza A is commonly found in birds, pigs, and…
revere | April 26, 2009The White House held a briefing this afternoon with the Secretary of Homeland Security, Acting Director of CDC and Nat'l Security adviser to the President in attendance. If you have been following this you wouldn't have learned much, but the overall tone was one of serious concern but steady confidence. It was good security theater, and I say that in a good way. Information was divulged (judging from some of the press questions there was no danger over estimating the knowledge of the audience) and a sensible plan described.
There are now officially 20 confirmed cases in the US in five states…
revere | April 26, 2009If there was ever a graphic illustration of how global interconnectedness affects public health, it's the swine flu affair. Wherever it started, the current crop of cases seems related to Mexico, either as the epicenter or via travelers. Four US states have cases. Those not on the Mexican border are related to travel to Mexico. Kansas, New York City, the suspect cases in secondary school teachers and students in Auckland, New Zealand just returned from Mexico. And France has two suspect cases also just returned from Mexico, as does Spain. We've discussed the problem of infectious disease on…
revere | April 25, 2009A concise summary of some additional developments, courtesy Bloomberg:
Three teachers and 22 students from Auckland’s Rangitoto high school are being tested for swine flu after returning to New Zealand’s most populous city from Los Angeles following a three week trip to Mexico, Stuff.co.nz reported on its Web site. Some of the travelers had symptoms of flu-like illness and were being isolated as a precaution pending test results, it said, citing the Auckland’s public health service.
In the U.K., a British Airways Plc crewmember with flu-like symptoms was taken to Northwick Park Hospital…
revere | April 25, 2009Canadian Press (Helen Branswell, with contributions from AP reporters) AP has a piece up about how Mexicans are coping that is worth a read, but we were drawn to this description of how the Mexican authorities first recognized something was amiss:.
Health authorities started noticing a threefold spike in flu cases in late March and early April, but they thought it was a late rebound in the December-February flu season.
Testing at domestic labs did not alert doctors here to the new strain, although U.S. authorities detected an outbreak in California and Texas last week.
Perhaps spurred by the…