General Epidemiology
tsmith | October 22, 2009I've written previously about "chicken pox parties". These types of events are coming back into vogue (they were common in the days before the vaccine, when the only way to provide immunity was to be infected), as parents mistakenly believe that "natural exposures" to these pathogens are somehow superior--and safer--than vaccinations. Though the latest rage are "H1N1 parties", chicken pox parties are still around, and potentially being held at your local McDonald's by families connecting on the internet:
I am trying to put together a chicken pox party and am looking for someone to donate…
tsmith | October 21, 2009I 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…
tsmith | September 18, 2009Taking a brief hiatus from my hiatus to discuss a question I've been asked a number of times in recent weeks by friends and family: what about flu shots? Are you getting one for yourself? Your kids? The answer is yes to both, with more explanation after the jump.
First, for readers unfamiliar with this blog, let me be frank regarding my opinion on vaccine "controversies," such as "vaccines cause autism." As I've discussed here several times already (and more can be found by searching my older posts), this assertion is completely unsupported by many scientific studies, so this is not a…
tsmith | May 4, 2009Back to the grind this week unfortunately, but the swine flu/H1N1 story is still developing and still fascinating. The most recent numbers show 286 confirmed US cases in 36 states.
There are many remaining questions on the evolution and epidemiology of this strain--and many pundits sure they know what's going to happen next. Mike takes one of them down--Wendy Orent, who I've blogged about previously. Orent is claiming (based on a black/white version of the evolution of virulence in pathogens) that the spread of this strain is attenuating the virus, and that future outbreaks will be…
tsmith | May 3, 2009Over 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…
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…
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…
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…
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,…
tsmith | April 27, 2009As 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…
tsmith | April 27, 2009For 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…
tsmith | April 26, 2009Over the last 24 hours, I've received a few comments and even more emails asking about or discussing the possibility of a "cytokine storm" triggered by the H1N1 swine flu reassortant. Is this what's happening in the cases from Mexico? Discussion after the jump...
Let me begin with a bit of background on what's meant by a "cytokine storm." In response to infection, the body has a number of ways to fight back against the invading microbe. Cytokines are one part of this defense. These are molecules produced by a number of different types of cells in response to infection that act as signals…
tsmith | April 25, 2009Sorry for the radio silence--I've been working on grants and manuscripts like a fiend, and so have tried to limit as many distractions as possible (which, unfortunately, includes blogging). However, the swine flu news is right up my alley, so I do just want to say a few words about it, and point you to some excellent stories already up elsewhere.
First, in case you've not been paying attention to the news in the last few days, there have been 8 reported cases of swine influenza infections in humans (6 in California and 2 in Texas, with additional suspected cases) and reports from Mexico…
tsmith | January 23, 2009 A little over a year ago I put a post up documenting research out of Canada which found methicillin-resistant Staphylococcus aureus (MRSA) in Canadian pigs. This had also been seen in Europe (with a lot of research coming out of the Netherlands). What I didn't note at the time was that we were gearing up to start some sampling of our own on area swine farms. Some of you saw that we presented the results of that research last year at ICEID and ASM; now the paper is out describing our pilot project in PLoS ONE. (Note: the paper was available earlier, but now they seem to have removed it…
tsmith | December 29, 2008As the Philippines requests international assistance to investigate the finding of Ebola Reston in their pigs, another human outbreak of Ebola has been confirmed in the Democratic Republic of Congo:
The Ministry of Health (MoH) of the Democratic Republic of the Congo declared on 25 December an outbreak of Ebola haemorrhagic fever in Mweka District, Kasai Occidental province based on laboratory results from the Centre International de Recherches Médicales de Franceville (CIRMF) in Gabon. CIRMF confirmed the presence of Ebola virus in 2 samples from 2 of the patients in the outbreak by antigen…
tsmith | December 11, 2008 I've mentioned repeatedly how little we know about Ebola ecology--what the reservoir host(s) are, how it's transmitted to humans (and other species), why it causes outbreaks when it does. We know even less about the Reston subtype of Ebola, which--in contrast to the Zaire, Sudan, Ivory Coast, and Bundibugyo subtypes, originated in Asia and was first found in monkeys imported into the United States for research purposes. It also is different from the other subtypes in that it appears to be only mildly lethal to monkeys, and several asymptomatic human infections have been documented (but…
tsmith | November 20, 2008 Few things can take me out of blogging hibernation (especially when the next grant deadline is Monday...) However, one of those things that I'll carve out time to write about is an interesting, hot-off-the-presses Ebola paper, and especially one describing a new strain of the virus--and there just happens to be such a paper in the new edition of PLoS Pathogens. Details after the jump...
Previously, 4 types of Ebola viruses had been identified. Ebola Zaire has typically been the worst as far as fatality rates (around 80-90%), with Ebola Sudan coming in close behind (roughly 50-70%). The…
tsmith | September 4, 2008 Oh, let's go back to the start... --Coldplay, "The Scientist"
A decade ago, a paper by Andrew Wakefield and colleagues was published in The Lancet, detailing the cases of 12 children with autism spectrum disorder (ASD). Anecdotal reports from parents of several of these children suggested that the onset of their condition followed receipt of the measles, mumps, and rubella (MMR) vaccine. Wakefield concluded following this research that the MMR vaccine was unsafe, and could play a causative role in the development of autism as well as gastrointestinal disease--the first volley in the…
tsmith | July 25, 2008
As I've mentioned, this has been a busy year. In the span of 3 months, 3 small grants were funded; enough to keep me busy for the next year. Though my training prior to arriving here was almost exclusively in bench microbiology (mostly molecular microbiology/molecular epidemiology), I knew when I took my current job that I wanted to expand that and go beyond just examining whatever samples someone else had on hand, and set up my own studies. Being Iowa, a big focus of our work is rural health and agriculture, so this has taken me out to cattle and pig farms--previously with a technician…
tsmith | July 23, 2008Revere once again is the voice of reason regarding latest developments in Tomatogate (e.g., the ongoing outbreak of Salmonella, serovar Saintpaul). Has the source been identified?
For those of you who many not have been following this closely, the outbreak has now hit almost every state, with over 1200 confirmed cases identified since April and more than 200 hospitalizations. Though the outbreak was initially associated with tomatoes, investigators were unable to link tomatoes to the specific strain--a relatively rare one--and advice to consumers to avoid varieties of tomatoes didn't put…