Fear & vaccines

I realize that, despite the scientific evidence to the contrary, there is still a lot of fear and misunderstanding about vaccine safety. Two recent articles discuss this “epidemic of fear” and why it affects us all, the first here at Wired magazine, and the second here at the Gotham Skeptic. I especially like the second, which has some excellent points:

My pediatric practice is situated at the nexus of three Manhattan neighborhoods (the West Village, Chelsea, and the Meat Packing District) that seem to comprise just the right balance of wealth, edginess, and socio-cultural awareness that lends itself to this new mistrust of vaccines. But these neighborhoods are not unique. According to sources at the NYC DOH, the Upper West Side of Manhattan and Park Slope in Brooklyn are also hot-spots of parental vaccine resistance. What stands out about these neighborhoods, and others like them, is that they contain a high percentage of middle to upper middle class families that tend to be young, well educated, and liberal in their political and social views. Because I live in one of these areas, work in another, and fit this description pretty squarely, I can identify with the underlying tendencies at work behind the concerns of these parents. A healthy questioning of authority (doctors), an underlying mistrust in the competence of the government (the CDC), overt mistrust and a general level of cynicism of big business (the pharmaceutical industry), and a sense of empowerment that comes with one’s social status, all contribute to this tendency to mistrust vaccines and those who recommend them. The difference between these concerned parents and myself (also a parent), is an understanding of the scientific method and the role it plays in this issue. One term that I have purposefully left out as a key element in this new epidemic is “skepticism.” While many of these parents believe they are being skeptical of vaccines, their manufacturers and the agencies that recommend them, this couldn’t be further from the truth. What they are being is misled and taken advantage of. They would actually be better characterized as anti-skeptics. To quote Brian Dunning of Skeptoid.com:

“The true meaning of the word skepticism has nothing to do with doubt, disbelief, or negativity. Skepticism is the process of applying reason and critical thinking to determine validity. It’s the process of finding a supported conclusion, not the justification of a preconceived conclusion.”

Why are the schools closing and other good H1N1 links…

Over at DailyKos, DemfromCT has an excellent post explaining why it may be beneficial for schools to close temporarily, even if they only have one confirmed case of swine influenza: H1N1: Why Do Schools Close, And When Do They Open?

DarkSyde also has one up on the basic biology and evolution of the flu.

Nick Kristof discusses our lack of attention to public health and what it means in the event of a pandemic in today’s NY Times.

[Updated: and via the comment theads, this post which further discusses what I mentioned here regarding testing–and how the confirmed cases are only the tip of the iceberg (complete with diagram!).

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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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: 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…

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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Swine flu update: Europe and the bottom of the world

For those of you looking to follow new cases (most of them suspected at this point, not confirmed), a great resource is HealthMap. Reports are popping up of possible infections worldwide: Scotland, Spain, Australia, and New Zealand. Certainly additional possible cases will be showing up over the coming days as well.

One thing I’ve seen mentioned (including here in the comments) is a question about the unlikelihood of a flu outbreak in Mexico in late April. Isn’t influenza a cold-weather bug? Well, yes and no. Influenza circulates year-round at a low level, but it lasts longer in the environment in colder temperatures with lower humidity, meaning more people can potentially be infected by each infected person, leading to our seasonal outbreaks. However, recall that in 1918 the first cases began in winter/spring 1918, and then it came back with a vengeance beginning in August, and really taking off by October. Additionally, we essentially have no barriers to worldwide spread, and there are already potential cases in New Zealand and Australia (where winter is setting in).

Again, we don’t know right now whether this will die out or become the next pandemic, but the spring timing of this doesn’t necessarily limit the virus’ potential.