influenza
sporte | May 2, 2009Nick's post on Amantadine resistance in swine flu was so interesting, I had to look at the protein structures myself.
I couldn't find any structures with the S31N mutation that Nick discussed, but I did find some structures with the M2 protein and Amantadine. Not only are these structures beautiful, but you can look at them and see how the protein works and how the drug prevents the protein from functioning.
As Nick mentions, the M2 protein from influenza makes a channel for hydrogen ions within the viral membrane. The channel controls the pH inside the virus by opening and closing.…
tsmith | May 1, 2009Nick Anthis has a very nice (and very readable!) overview of why flu viruses (including the new A/H1N1 strain) are resistant to adamantane, one of the antiviral drugs that can be used to treat influenza infections.
mikethemadbiologist | May 1, 2009For keeping the big picture in mind when it comes to influenza--as the CDC decides to proceed with seasonal influenza vaccine production:
Dr. Marc Lipsitch, a Harvard School of Public Health epidemiologist, said the decision to proceed with seasonal flu vaccine production is evidence "that garden-variety seasonal flu kills on the order of 36,000 people a year, and while we are in a crisis and it might seem to make sense to ignore that, you can't."
..."We want to make sure in the vaccine manufacturing that we were still able to protect the country from seasonal flu and be able to protect from…
tsmith | April 30, 2009I've been seeing a lot of comments mocking the current outbreak of H1N1, and a lot of people (and journalists) who don't understand what "big deal" is about the "snoutbreak" of swine influenza, or don't get what the raising of the World Health Organization's pandemic alert phase up to 5 means. I noted here what the alert level meant, but wanted to discuss it a bit more in a full post; after the jump.
So, some comments I've seen thrown about:
This is all just media hype! Lies about the Mexican cases! The WHO just revised their numbers down to 26 cases and 7 deaths! Why should I believe…
sporte | April 30, 2009Last night, the phone rang at 9:22 pm. I quickly glanced at the caller ID. Hmmm. Why is the Seattle School district calling us at this time of night?
Apparently the swine flu has come to Seattle and the school district thought we should know.
Those messages are helpful if you're a parent, but they don't tell much about the rest of the world.
Health Map is a really wonderful, user-friendly, resource for following the epidemic.
When you get to Health Map , choose Select None to clear the map.
Then select Swine Flu.
You'll see a Google map with markers representing reports. The colors show…
tsmith | April 29, 2009It was only a matter of time:
Iowa Gov. Chet Culver says the state has two probable causes of swine flu.
Speaking Wednesday at a Statehouse news conference, Culver told reporters that officials would know Thursday if the cases are swine flu.
Officials say one case was from a California resident who visited Scott and Clinton counties last week. The other was a woman who returned from Mexico and traveled through Johnson, Des Moines and Muscatine counties.
State Medical Director Patricia Quinlisk says both of the people infected were now recovering.
Should know by tomorrow if they are confirmed…
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.
tsmith | April 29, 2009Brandon Keim at WiredScience has a new article on swine flu genomics.
"This is what we call a reassortment between two currently circulating pig flu viruses," said Andrew Rambaut, a University of Edinburgh viral geneticist. "Why it's emerged in humans is anyone's guess. It hasn't been seen before in pigs as far as I know."
***
"The new neuraminidase gene that came in from Eurasian swine is one we've never before seen circulating in humans," said Rambaut. "That's one of the reasons it's spreading rapidly. Very few people will have any immunity to this particular combination, which is what…
tsmith | April 29, 2009The latest numbers of confirmed cases from the CDC were released about an hour ago. 91 cases have been confirmed, with the largest numbers in New York (51), California (14), and Texas (16). One new case has also been confirmed in Nevada, one in Indiana, one in Arizona, and 2 in Michigan; the other Ohio case I know of is still pending, apparently. Ongoing investigations are also taking place in multiple states, so expect the number to keep rising for the time being. [Update: 2 cases just confirmed in Massachussets, and three in Maine.]
The first fatality has also been reported: a 23-month-…
mikethemadbiologist | April 29, 2009Probably not. I have no idea how serious this swine flu outbreak will be. As I noted yesterday, it could evolve to cause less severe symptoms or more severe symptoms--right now, nobody knows for certain. But I find the possible overreaction by the public to be disturbing (I think the public health system has adopted the right tone--and kudos, in part, to Richard Besser. Gerbeding who?). Why?
Every year, roughly 36,000 people die from seasonal (or annual influenza). That's double HIV/AIDS deaths. But nobody gets paranoid about handwashing (WASH YOUR DAMN HANDS!!). There's no serious…
tsmith | April 28, 2009Back in 2007, I wrote about an outbreak of swine influenza from an Ohio county fair. The peer-reviewed paper analyzing the swine influenza isolated from that outbreak has just recently come out. From the abstract:
The swine isolate, A/SW/OH/511445/2007 (OH07), was evaluated in an experimental challenge and transmission study reported here. Our results indicate that the OH07 virus was pathogenic in pigs, was transmissible among pigs, and failed to cross-react with many swine H1 anti-sera. Naturally exposed pigs shed virus as early as 3 days and as long as 7 days after contact with…
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…
tsmith | April 28, 2009Revere on quarantine versus isolation. This is a topic I've covered previously (here) as well, and an important distinction (though the two are often muddled together in the press).
Christine Gorman talks about getting the facts straight on swine flu, and offers up many additional resources to keep you updated.
Skepchick provides "Things More Likely to Save You From Swine Flu Than Homeopathy". Colon cleanse and chiropractic are noticeably absent...
1976 swine flu Public Service Announcements. They don't make 'em like that anymore... (h/t http://twitter.com/tomburket)
Finally, my…
tsmith | April 28, 2009Stories in Spanish: Costa Rica becomes the first Central American country to confirm swine flu ("gripe porcina"). A 21 year old who had traveled to Mexico is in stable condition. An additional 16 cases were examined but were negative. Brazil is also examining 11 travelers; cases are also being examined in Panama, Honduras, Argentina, and Uruguay, and Chile.
In Asia, South Korea is examining a possible case, while China's stepped up its efforts to look for cases (and blocked import of pork from the US and Mexico).
Most of the cases that are being examined have traveled to Mexico…
mikethemadbiologist | April 28, 2009Surly Amy mixes swine flu and homeopathy:
Do you suppose the homeopaths are diluting a smidgen of a pig in water right now?
See, Twitter does have its uses....
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…
tsmith | April 28, 2009I was introduced to snake oil salesmen at a young age. My mother was diagnosed with multiple sclerosis when I was in kindergarten, and while she has mostly followed the advice of her neurologists, she's also looked into "alternate" therapies, ranging from the relatively harmless (massages, oils, etc.) to more invasive methods (chelation, all sorts of expensive but worthless supplements). Some of these I've been able to talk her out of (and I personally think her current doctor--NOT a neurologist--is a total quack), but others she's taken because, hey, "what's the harm?" It's frustrating to…
mikethemadbiologist | April 28, 2009Since TEH SWINE FLU!!!11!!! is a hot topic, I thought this post about how infections could evolve increased virulence after switching animal hosts was relevant. From the Murky Depths of the Mad Biologist's Archives: There's no reason to think that an epidemic influenza strain won't become more deadly....
Several people have argued that if an influenza pandemic were to occur, it will rapidly evolve to become less virulent--that is less deadly. A recent paper explains why this might be wrong.
Basically, the flaw with the 'optimistic' argument is that it is assumes that the virus will be…
tsmith | April 27, 2009...asked Joe. Answer: only a few days to sequence, clean up the data, and submit to NCBI. Seven H1N1 swine flu sequences are up (H/T Jonathan Eisen). I've not had a chance to crack anything open yet, but I hope to see some analysis from more of the genomics geeks soon...However, one bummer is that they don't have any from the Mexico cases available--and particularly, any sequence data from any of the fatal cases. These will be helpful to see if there are any point mutations that could possibly account for a virulence difference between the Mexican and US cases. (Unlikely, I'd guess,…
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…