swine flu
bioephemera | April 29, 2009Let etsy seller foliage help you fight swine flu with this bagful of handmade soaps in "skin-ish colors"!
I vascillate between finding them cute, and thinking they resemble a crowd of damned souls reaching out for help from my soap dish. Weird.
Dedicated to John O., who truly appreciates disembodied hands. Via DailyArtMuse.
revere | April 29, 2009This has been a supremely frustrating day for me since I am traveling and must attend to professional business having nothing to do with the current outbreak. I is incredibly maddening to be away from fast moving events. I'll return home Friday night. In the meantime I will do what I can late in the day and early in the morning, and if I can't sleep, in the middle of the night. Since there are plenty of other places paying attention you'll still be getting the latest news and I am hoping the enforced distancing may allow me to give a more detached view. That aside, I have a favor to ask of…
ddobbs | April 29, 2009
It'd be nice to think otherwise. But even as WHO moves to Phase 5, recognizing that there is sustained human-to-human spread of this virus, we're still not sure how much punch it has. Which, as SophieZoe points out at A Pandemic Chronicle doesn't leave us with much :
Beyond the change in the official alert level we know no more today than we knew yesterday, which was pretty much nothing at all.
We do not yet know how the virus is going to behave in the general population and how severe or mild the disease will be on average. We do not even know if the virus will show %u201Csticking power%…
sporte | April 29, 2009I'm teaching an on-line bioinformatics course this semester for Austin Community College. They are in Texas of course, but I am in Seattle. This presents a few interesting challenges and some minor moments of amusement.
Today, the school sent all the faculty emails telling us to stay home if we're sick.
Got it. If I think I have flu, I will not fly to Texas.
Instead, I'll stay home and watch videos on coughing without contaminating others.
Watch "Why don't we do it in our sleeves?" and find out how you rank on the safe coughing scale.
revere | April 29, 2009As is usual (routine? no, nothing routine about this) in an evolving epidemic contradictory and confusing numbers are appearing. Some of them are the result of information lags (tallies not being updated), some are the result of using different criteria for counting (suspect versus probable versus lab confirmed, etc.), some are just rumors. WHO is saying that in Mexico there are only 7 confirmed deaths, 19 more lab confirmed cases, 159 probable cases and some 1300 being evaluated, based on official reporting to them by officials of a member state, the Mexico. Everyone knows there are many…
ddobbs | April 29, 2009Revere reminds us of how isolation and quarantine are not the same:
Both Avian Flu Diary and H5N1 look at how Mexico's 160+ "swine flu deaths" got knocked back to just 7.
Andre Picard (why do so many ace flu reporters come out of Canada?) argues we should Keep the fear-o-meter on low for now
ZDNet Healthcare chides the media for not doing so.
CIDRAP launches a breaking news tracker.
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The Vancouver Sun finds a sunny angle on the 1918 flu.
Nature provides a timeline.
sporte | April 29, 2009What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu?
If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer.
Activity 4. Picking influenza sequences and comparing them with phylogenetic trees
We can get the genome sequences, piece by piece, as I described in earlier, but the NCBI has other tools that are useful, too.
The Influenza Virus Resource will let us pick sequences, align them, and make trees so we can quickly compare the sequences to each other.
This is how I got the sequences that I wrote about…
gregladen | April 29, 2009
The swine flu maneno in the 1970s was actually a key moment in the history of epidemiology politics. It also relates to the history of anti-vaccine activism in important and interesting ways. I should probably write a whole post about it. For now, suffice it to say that the government reaction to the sudden appearance of swine flu on the scene was somewhat bungled, it is probably true that the wrong people got screwed, and the swine flu itself turned out to be a false start. But please also note that the epidemiology of the present swine flu is very different from what we had then. And…
ddobbs | April 29, 2009This swine flu business is moving fast now, with confirmed or reported cases popping up everywhere and the first reported death outside Mexico -- a 23-month-old child in Texas -- reported this morning. As Effect Measure notes
Some of the fear [generated in the U.S. by this deat] will be lessened by the new knowledge that the baby contracted the disease in another country. The empathy remains, as it should. Mexican babies are still babies, loved by their parents and grandparents even while being hostages to fortune like everyone.
As this outbreak moves forward we will be barraged by numbers…
revere | April 29, 2009The first death in the US from swine flu in a Texas toddler is being widely reported, but a piece just in from Bloomberg says the infection was acquired in Mexico:
The first confirmed U.S. swine flu death was a 22-month-old child from Mexico, according to a Houston official.
The toddler was brought to Houston for medical care last weekend and died on Monday, Kathy Barton, spokeswoman for the Houston Department of Health and Human Services said today in an interview. (Mary Schlangenstein, Bloomberg)
The national origin of the victim is of some epidemiological import but irrelevant to the human…
grrlscientist | April 29, 2009tags: Antigen Shift, Influenza Viruses, molecular biology, virology, microbiology, streaming video
This video discusses the process of antigen shift in influenza viruses, such as the H1N1 "swine flu" that has recently been identified in Mexico and in quite a few other countries, including in NYC [1:18]
palmd | April 29, 2009Here at ScienceBlogs we have a (very) informal agreement to try to avoid profanity-laden titles. Personally, they don't bother me at all, but I can see the point---there are lots of folks who probably don't want their feed reader to pop up with what I'm about to say.
What the FUCK hath swine flu wrought????
I warned you that swine flu would bring out the charlatans. In the course of hours to days, a virtual zombie army of immoral, idiotic, evil fucking quacks has risen to fan your fears and take you cash.
It's really hard to overstate this, but the people who engage in this fact- and…
razib | April 28, 2009Swine influenza, seasonality, and the northern hemisphere:
This history demonstrates the seasonality of pandemic influenza, and suggesta that spread of A/California/09/2009 in the northern hemisphere is not imminent. Based on this regularity, the epidemic in Mexico should be over no later than the end of May. While it is not 'impossible to see the current contagion spreading in the northern hemisphere over the following months', it would be unprecedented.
razib | April 28, 2009That's what Sandy at Digital Biology is suggesting from her analyses.... (also see Tara of Aetiology's response)
sporte | April 28, 2009This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair.
UPDATE: I'm not so certain anymore that the strains are the same. I'm doing some work with nucleic acid sequences to look further at similarity.
Here's the data.
Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look.
And, like eating potato chips, making phylogenetic trees is a little bit…
revere | April 28, 2009CDC guidelines for antiviral therapy for swine flu infection:
This swine influenza A (H1N1) virus is sensitive (susceptible) to the neuraminidase inhibitor antiviral medications zanamivir and oseltamivir. It is resistant to the adamantane antiviral medications, amantadine and rimantadine. (CDC)
What are these antiviral drugs and how do they work? Over the years here we've discussed this pretty often, so I went back and retrieved one of our older posts (from 2007). I've done some editing but it's pretty much the same as when I wrote it about bird flu. Same principles.
Oseltamivir (which we…
ddobbs | April 28, 2009Via emails, comments, and so on, quite a few people offered their own explanations for why mortality might be higher in Mexico (as of yesterday), the subject of my Slate piece.
First, though, a correction: I punched my numbers a bit too quickly in computing the flue's hypothetical kill ratios in Mexico, and had everything a decimal point over, and -- and therefore tenfold too understated.
Alert reader johnshade called this to my attention:
You'll want to fix your own "bad math":
"about 100 deaths?suggesting a mortality rate of 6 percent. This is
almost certainly bad math, as the total case…
sporte | April 28, 2009I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI.
You can get them and work them, too. It's pretty easy. Tomorrow, we'll align sequences and make trees.
Activity 3: Getting the swine flu sequence data
1. Go to the NCBI, find the Influenza Virus Resource page and follow the link to:
04/27/2009: Newest swine influenza A (H1N1) sequences.
2. You'll see a page that looks like this:
Each column heading is a name of a segment of the influenza genome. You can see there are eight of these. Each segment…
revere | April 28, 2009As cases continue to accrue in different places we will hear more talk about quarantine and isolation. These are two terms that are frequently confused, which is too bad, because isolation makes sense for influenza and quarantine doesn't. So what do they mean?
What quarantine and isolation have in common is they are both designed to interrupt the transmission of a disease that spreads from person to person. Quarantine is the legally enforceable segregation of people who people who have been or may have been exposed but who aren't (yet) sick. Some people talk about "voluntary quarantines," but…
sporte | April 28, 2009I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases.
In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly, but...
Now, you might wonder, what kinds of flu do these different creatures get? Are they all getting H1N1, or do they get different variations? What are H and N anyway?
We can discuss all of these, but for now, lets see what kinds of flu strains infect different kinds of creatures.
Activity 2. What flu infects…