What does the WHO’s pandemic scale mean? And why is anyone worried about this?

I’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.
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Iowa investigating two “probable” swine flu cases

It 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 or not.

Wired: H1N1 a hybrid of 2 pig isolates

Brandon 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 gives the concern that this will be a pandemic rather than just a normal seasonal flu outbreak. It remains to be seen how much and to what extent there is existing immunity.”

Story still evolving…Keim does mention that “a document released to scientists and obtained by Wired.com affirms their analysis.” Could be out in the literature soon, possibly?

I was hoping to have a post up today with more thoughts on the whole pig issue, but no time to do anything but quick posts. Hopefully tomorrow…

US up to 91 cases, including 1 death [Updated: New England confirmed cases]

The 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-old child who had recently traveled to Mexico traveled to the United States from Mexico.

I’ve written previously about how difficult research in infectious disease can sometimes be, knowing that many of the isolates you’re working with harmed or even killed someone, and changed someone’s life forever. This child’s influenza virus will now be marked with a lengthy name based on the date and location of isolation, and will be studied and dissected on a molecular level, and referred to in dry publications discussing the case–but that doesn’t mean that those who carry out the research and write up the manuscripts in such clinical language are any less touched and upset when deaths like this occur.

Swine flu–deja vu all over again?

Back 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 experimentally infected pigs. This suggests there was opportunity for exposure of people handling the pigs at the fair. The molecular analysis of the OH07 isolates demonstrated that the eight gene segments were similar to those of currently circulating triple reassortant swine influenza viruses. However, numerous nucleotide changes leading to amino acid changes were demonstrated in the HA gene and throughout the genome as compared to contemporary swine viruses in the same genetic cluster. It remains unknown if any of the amino acid changes were related to the ability of this virus to infect people. The characteristics of the OH07 virus in our pig experimental model as well as the documented human transmission warrant close monitoring of the spread of this virus in pig and human populations.

Meanwhile, I mentioned yesterday that gene sequences from the new H1N1 virus had been released. Sandy has taken a look at some of these, and compared them with H1N1 and H1N2 viruses from humans and pigs.

Yes, there is a point to the juxtaposition of these two points, and it’s big–after the jump…
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Swine flu link roundup

Revere 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 colleague, Dan Diekema, a hospital epidemiologist extraordinaire here at the University of Iowa, has started a new blog: Controversies in Hospital Infection Prevention. Obviously, swine flu has been the big discussion in this area over the last few days, and Dan and his co-blogger, Michael Edmond, have several posts on swine flu and infection control. Stop by and check it out…

Swine flu: Central & South America, Asia, New York update

Stories 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 recently, but secondary spread may be occurring in New York City. 45 cases have been confirmed to date, but many more are suspected or have been alluded to in news reports. This extended human-to-human chain of transmission is the worrisome part–if this is efficient, it’s going to be much more difficult to get ahead of the virus and minimize spread. Expect much focus in the coming days and weeks to be on contacts of infected cases, in an effort to determine the frequency of secondary transmission…

Swine flu and snake oil

I 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 see money and hope wasted on bogus treatments.

Of course, it’s not only chronic conditions that appeal to these salesmen; they’re all over infectious disease as well, peddling unproven treatments to “boost the immune system” and discouraging the use of conventional treatments. It appears that swine flu is their newest target (h/t Orac), as chiropractic is said to have “miraculous” results and colon cleanses, likewise, “work miracles”. The authors both suggest that their fave treatment, therefore, should also be used to treat/prevent swine flu. After all, claims Kim Evans (author of Cleaning Up! and the creator of The Cleaning Up! Cleanse, a powerful body cleanse):

And it’s my understanding that many people who took regular enemas instead of vaccines during the 1918 pandemic made it out on the other side as well.

Ah, someone has been studying up on their Whale.to 1918 flu pandemic revisionist epidemiology. Fantastic.

Seriously, HuffPost? This is what you want to promote? What’s next–lizard men?

How long does it take to sequence an influenza virus?

…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, but it would be nice to check it out…)

Swine flu–still spreading

As expected, new potential cases are being investigated in several states, including an additional possible case in Northern California, 2 potential cases in Indiana, a potential case in Ohio and another in Michigan [updated: and some in Massachusetts too]. New York has also confirmed 20 cases now, and 17 more are suspected (check here for additional information–updated as new cases come in and are confirmed or ruled out). Around the world, four in France have apparently tested negative, as have two potential cases in Australia, while 2 in Scotland have been confirmed positive. In Mexico, the current numbers put it at over 100 deaths and above 1600 suspected cases (again, not all of those laboratory confirmed).

(More on these after the jump…)
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