epidemiology
revere | July 2, 2009The first cases of swine flu were diagnosed in the US in San Diego in mid-April. The discovery was serendipitous, the result of out-of-season US-Mexican border surveillance and use of a new diagnostic test at the Naval Health Research Center. When the new test protocol showed infection with influenza A with undeterminable subtype, follow-up testing showed it to be an previously unknown swine flu virus. Detection of a second, apparently unlinked swine flu infection in San Diego got the outbreak (now pandemic) investigation rolling.
That was just over 2 months ago, but it established the…
revere | July 1, 2009For reasons not revealed to anyone I know, WHO is saying the Tamiflu resistance in a Danish swine flu isolate is "isolated case." Could be, but I'd sure like to know why they think so, other than they don't have any other examples. Meanwhile WHO and CDC continue to advise prompt use of Tamiflu (oral oseltamivir) for treatment of swine flu in high risk patients. Which brings up the question of side effects.
The most common Tamiflu side effect is nausea and vomiting. When my daughter was seen at the local hospital ER for swine flu symptoms and a positive rapid test for influenza A at a time…
revere | June 19, 2009Swine flu infection of health care workers (or as CDC refers to them, health care personnel or HCP) was of interest early in the pre-pandemic phase for at last two reasons. One was the obvious goal of estimating the risk to front line workers and devising best practices for their protection. Another was the belief, reinforced by the SARS outbreak in 2003, that spread to HCP was an early warning that the virus was easily transmissible from person to person. SARS is a disease where patients are most infectious in the later stages when they are extremely ill, and HCP were among the hardest hit…
revere | June 5, 2009In New York City, an illness termed "mild" for many has killed 7 and put 300 in the hospital. A preliminary analysis of about half of those hospitalized, most (82%) were said to have some underlying medical condition. That's common with flu, but it's also a reminder that one of five were otherwise healthy, and unusually for flu, most of them relatively young (mostly under 65). Similarly, the deaths also had underlying medical conditions but were relatively young (median age 43). The two most recent deaths were in the mid 40s.
So not being old is one risk factor. What does "underlying medical…
grrlscientist | June 4, 2009tags: NYC, New York City, Manhattan, swine flu, influenza, A/H1N1 Influenza, New York Academy of Sciences, NYAS
This is an overview of the NYAS symposium about Influenza A/H1N1 "swine flu" outbreak that I was invited to attend on 28 May 2009 in NYC.
Under the auspices of the New York Academy of Sciences' Emerging Infectious Diseases and Microbiology Discussion Group, vaccine experts, epidemiologists, and policymakers from around the United States met in New York City to discuss the current outbreak of Influenza A/H1N1 -- "swine flu." The program presented information about influenza…
grrlscientist | May 28, 2009
[larger view]
The New York Academy of Sciences hosted a symposium yesterday in the World Trade Center that explored the latest findings associated with "swine flu", more correctly known as the A/H1N1 Influenza. This symposium was broadcast live as a "webinar" and is also being made into a podcast and streaming video (both of which will be available next week, and which I will be linking to). This photoessay shows some of the preparations carried out for this event. I am working on more substantive essays and they should be published here beginning next week.
As you can see in the above…
grrlscientist | May 28, 2009Because of my affiliation with ScienceBlogs and SEED Media Group, I am attending a symposium hosted by the New York Academy of Sciences (NYAS) that focuses on H1N1 Influenza [website].
This symposium will explore the 2009 H1N1 (swine) Influenza outbreak by hosting presentations on the new recombinant virus, epidemiology, treatment, vaccine development and the public health implications of a worldwide pandemic [PDF].
This event is also being held as a live, streaming Webinar and this recording, I am told, will be available for the general public to access sometime next week. I will be taking…
grrlscientist | May 28, 2009tags: TEDTalks, virology, epidemiology, Nathan Wolfe, SARS, Influenza, streaming video
I am very lucky to be attending a New York Academy of Science (NYAS) conference about H1N1 Influenza today, so I thought I'd share this TEDTalk video about viral outbreaks, a talk presented by virus hunter Nathan Wolfe. His goal? Outwitting the next pandemic by staying two steps ahead: discovering new, deadly viruses where they first emerge -- passing from animals to humans among poor subsistence hunters in Africa -- and stopping them before they claim millions of lives. [13:05]
revere | May 28, 2009Influenza surveillance in the US has at least five component parts (depending on how you count it is as many as seven). We discussed the virologic surveillance system in another post. CDC has two surveillance sub-systems that look at hospitalized cases with laboratory confirmed influenza, the New Vaccine Surveillance Network (NVSN) and the Emerging Infections Program (EIP). The NVSN is confined to cases in children less than five years old, while the EIP covers all ages. Let's take a look at the most recent EIP data.
EIP doesn't cover the entire country. Instead it collects data from 60…
revere | May 22, 2009There is as yet no vaccine for the novel H1N1 (swine flu) pandemic strain of influenza now causing widespread illness in North America and what appears to be the start of growing outbreaks in Japan and parts of Europe (but check out this excellent piece over at ScienceInsider). WHO says most developing nations are not able to track influenza, so what is happening in Africa and parts of Asia is not known with any confidence. While the clinical illness from this virus doesn't seem very different than seasonal flu, the fact that most of the world's population has no immunity to it means there is…
revere | May 13, 2009Over at ScienceInsider (Science magazine's blog) Jon Cohen speculates about why swine flu seems to have spread faster and more widely in North America (Mexicon, US, Canada) than Europe and Asia. CDC thinks one reason is that by the time it was discovered here it had already spread widely. The Europeans, with advance warning, were then able to contain it with aggressive use of antivirals among travelers from the affected areas. I'm not ready to buy this.
This doesn't make sense to me, although nothing about flu viruses make sense, so I could be wrong about this. But it wouldn't explain why…
revere | May 12, 2009Trying to figure out where the incipient swine flu pandemic is heading and how fast it is heading there is shooting at a moving target, and this one is moving pretty fast. The best we can do at this point is use whatever information we have to make some educated guesses about different scenarios along with how likely various scenarios are. We used to do this on the back of an envelope, Now we use computer programs. I'm not sure we are doing much better (or much worse), but we can make use of more information and the answer looks prettier when displayed.
Expedited publication of such an…
revere | May 8, 2009Late yesterday The New England Journal of Medicine published a number of papers on the recent swine flu outbreak. The first paper, "Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans" by large federal-state team of epidemiologists describes 642 confirmed cases in 41 states as of May 5, 2009, two days before publication. What I find remarkable is the speed the problem was recognized -- literally days. Identification of the virus was first made in the CDC laboratory on April 15, just 3 weeks ago. Now we are already reading scientific papers providing a wealth of detail.
Among…
grrlscientist | May 7, 2009tags: TEDTalks, Laurie Garrett, H5N1 Influenza, influenza, virology, epidemics, streaming video
Recorded in 2007, as the world worried about a possible avian flu epidemic, Laurie Garrett, author of "The Coming Plague," gave this powerful talk to a small TED University audience. Her insights from past pandemics are suddenly more relevant than ever. [21:05]
revere | May 6, 2009How fast flu spreads is related to how many susceptible people an infectious person can infect (a measure called R0) and also something called the serial interval. The serial interval is the average length of time between the start of one infection and the start of the infection of that case's infected contacts. The horter the serial interval the faster a virus can spread. So what is the serial interval for this virus and how can we determine it? The answer to the first question is the usual. We don't know yet. The answer to the second one tells us a little about why we don't know and why we…
revere | April 30, 2009There is a tendency to be preoccupied with the latest in fast moving events, but I want to pause for a moment to make a point that has been lost in the discussion: we are witnessing a medical science landmark. Never before have we watched a flu outbreak of global dimensions unfold in real time. Nor have we ever had the opportunity to alter the course of such an outbreak.
I have been critical of WHO for being late to the party, but they are fully on board now and by raising the pandemic threat level to phase 5 have done something very important: served notice that it's time to mobilize…
revere | April 29, 2009As is usual (routine? no, nothing routine about this) in an evolving epidemic contradictory and confusing numbers are appearing. Some of them are the result of information lags (tallies not being updated), some are the result of using different criteria for counting (suspect versus probable versus lab confirmed, etc.), some are just rumors. WHO is saying that in Mexico there are only 7 confirmed deaths, 19 more lab confirmed cases, 159 probable cases and some 1300 being evaluated, based on official reporting to them by officials of a member state, the Mexico. Everyone knows there are many…
ddobbs | April 29, 2009This swine flu business is moving fast now, with confirmed or reported cases popping up everywhere and the first reported death outside Mexico -- a 23-month-old child in Texas -- reported this morning. As Effect Measure notes
Some of the fear [generated in the U.S. by this deat] will be lessened by the new knowledge that the baby contracted the disease in another country. The empathy remains, as it should. Mexican babies are still babies, loved by their parents and grandparents even while being hostages to fortune like everyone.
As this outbreak moves forward we will be barraged by numbers…
revere | April 28, 2009It would be nice to think that the 28 cases at the NY Prep School are it for the city and that the virus has been contained there. But that was always more a wish than a plausible reality:
CBS 2 HD has learned of a confirmed case of swine flu at the Ernst & Young headquarters in Times Square.
One of the staffers became ill over the weekend after coming into contact with a family member who had been exposed to the virus.
The staffer is said to be resting at home and the company believes, due to the virus' 24-hour incubation period, that no one else at Ernst & Young was exposed. The…
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…