infectious disease
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,…
revere | April 27, 2009One of the things we'd like to know about the swine flu virus is its Case Fatality Ratio (CFR, commonly called a case fatality rate, although it isn't technically a rate but a proportion). But what is a CFR? And how is it different from a mortality rate?
The CFR is an estimate of the probability that someone with the swine flu will die of it (technically, before dying from something else or recovering). The higher the CFR, the more virulent the virus. So what's virulence? Virulence refers to the severity of the disease the virus produces. Rabies is a virulent virus. Everybody dies from it…
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…
revere | April 27, 2009The daily CDC conference call was not particularly informative, but these daily briefings are still extremely valuable. Things are happening fairly fast but nothing we didn't expect. There are now 40 confirmed US cases in the same 5 states (California, NY, Texas, Kansas, Ohio). The 28 new cases sere contributed by the New York prep school that had the state's first 8 cases. These additional ones are the result of continued case finding. Acting CDC Director said that the only laboratory confirmed human to human transmission is in the Kansas husband and wife (he had just returned from Mexico…
revere | April 27, 2009Usually "What did you expect?" is a rhetorical question, but we have a more serious point to make. Let's start with the familiar and move on to the less familiar. Many of you are coming here to find the latest news about swine flu. It's an imprecise term that covers two different things: what has happened that is new, in the sense of surprising and we didn't already know it would happen; and what is the current situation. Overnight (in the US) Europe (Spain) registered its first confirmed case. That's additional data but not surprising. We know this virus is seeded out there and we shouldn't…
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…
revere | April 26, 2009The White House briefing today had Obama written all over it. It's themes were Obama, it's tone of quiet, serious confidence were Obama. The sense of total command of the situation was Obama. There was the Obama-ese call for "personal responsibility." Government can't do everything. There are things we each have to take personal responsibility for.
Fine. I don't disagree. But I think there are some things missing from this frame. One is that it isn't a binary choice, government or the individual. We all live in a set of overlapping communities: work, home, neighborhood, civic organizations,…
revere | April 26, 2009The White House held a briefing this afternoon with the Secretary of Homeland Security, Acting Director of CDC and Nat'l Security adviser to the President in attendance. If you have been following this you wouldn't have learned much, but the overall tone was one of serious concern but steady confidence. It was good security theater, and I say that in a good way. Information was divulged (judging from some of the press questions there was no danger over estimating the knowledge of the audience) and a sensible plan described.
There are now officially 20 confirmed cases in the US in five states…
revere | April 26, 2009If there was ever a graphic illustration of how global interconnectedness affects public health, it's the swine flu affair. Wherever it started, the current crop of cases seems related to Mexico, either as the epicenter or via travelers. Four US states have cases. Those not on the Mexican border are related to travel to Mexico. Kansas, New York City, the suspect cases in secondary school teachers and students in Auckland, New Zealand just returned from Mexico. And France has two suspect cases also just returned from Mexico, as does Spain. We've discussed the problem of infectious disease on…
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…
revere | April 25, 2009A concise summary of some additional developments, courtesy Bloomberg:
Three teachers and 22 students from Auckland’s Rangitoto high school are being tested for swine flu after returning to New Zealand’s most populous city from Los Angeles following a three week trip to Mexico, Stuff.co.nz reported on its Web site. Some of the travelers had symptoms of flu-like illness and were being isolated as a precaution pending test results, it said, citing the Auckland’s public health service.
In the U.K., a British Airways Plc crewmember with flu-like symptoms was taken to Northwick Park Hospital…
revere | April 25, 2009Canadian Press (Helen Branswell, with contributions from AP reporters) AP has a piece up about how Mexicans are coping that is worth a read, but we were drawn to this description of how the Mexican authorities first recognized something was amiss:.
Health authorities started noticing a threefold spike in flu cases in late March and early April, but they thought it was a late rebound in the December-February flu season.
Testing at domestic labs did not alert doctors here to the new strain, although U.S. authorities detected an outbreak in California and Texas last week.
Perhaps spurred by the…
revere | April 25, 2009There may not have been much news at the CDC briefing, but it is coming thick and fast now. The CDC works through state health departments and defers to them on information about what is going on in their localities. Hence all questions about this were deflected at the 1 pm CDC briefing. I think I understand the thinking behind this but it doesn't serve the goal of getting the information out there quickly. CDC needs to be the information clearing house for all the swine flu news going on around the country and they need to do with absolute transparency. Here's what has developed since that…
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…
revere | April 25, 2009CDC has just concluded a press briefing and the big news is there is no big news. In fact there was hardly any small news. The major questions have been identified -- how transmissible, what is the epidemic curve, are there more cases in the US, are there subtle genetic differences in the US and Mexican versions to account for the apparent difference in clinical and epidemiological features, etc. -- but answering them will take longer.
Meanwhile, no new cases have been identified in the US, but CDC in collaboration with state and local health departments and the academic and medical sectors…
revere | April 25, 2009There will be an update from CDC later today and WHO's expert committee established under the new International Health Regulations (IHR) meets via teleconference this morning North American east coast time at 10 am (4 pm Geneva time) to consider whether the swine flu situation merits declaring it “a public health event of international concern.” If they do, WHO Director General Margaret Chan may respond by raising the pandemic threat alert level from the current phase 3 (new virus: no or limited human to human transmission) to phase 4 (new virus, evidence of increased human to human…
revere | April 24, 2009Some end-of-the day (but not end-of-the-world) bits and pieces in the emerging swine flu story.
From Helen Branswell (Canadian Press):
In Mexico, Secretary of Health Jose Angel Cordova Villalobos said in a television interview that there have been 45 deaths, but only 16 of those were directly related to the flu in question.
An estimated 943 people are ill, the television report said.
The majority of the cases are occurring in young, previously healthy adults in their mid 20s to mid 40s, reports suggest. Experts aren’t certain if all of those people are sick with this virus or if other flu or…
revere | April 24, 2009Two recent sources of information, a conference call for clinicians and a just concluded media conference call held by CDC Acting Director Richard Besser.
Clinician call:
An emergency conference call for the Clinician Outreach and Communication Activity (COCA) was announced just hours ago on the Clinicians Terrorism and Emergency Preparedness listserv. It was "live blogged" via the Comments Thread by reader Abigail, MD. Here's the gist (lightly edited), as typed by her in real time (thanks!):
Update on current emergency situation - 8 individuals in US with swine flu, the hospitalized patient…
revere | April 24, 2009Friday April 24, 1:40 pm: AP and NYT reporting that Mexican authorities are saying that they have determined that 16 of 60 deaths are "swine flu," with 44 more being tested. They have yet to confirm whether it is the same as the California/Texas cases, but that's a bit irrelevant since either way it sounds like a very worrisome development. There are already a reported 930 plus cases, with schools closed in Mexico City and contemplation of closing government offices. Obama has been notified and the White House is following the situation. WHO and CDC have activated their emergency centers and…