Surveillance

Swine 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…
However this pandemic evolves, we are going to learn a lot about how pandemics evolve -- or maybe even start. A paper just published online in Nature sets out a bit more of what we know about this pandemic strain (yes, we can officially refer to it that way now) and makes some observations about its prehistory (its history before it became known and documented by we mortals). Maryn McKenna has an excellent run-down over at CIDRAP News, which you should read. Here's our take on it. First, we'd like to make a "meta-science" observation. This paper is unusual in several ways. The least…
An interesting piece on an infection trial of novel H1N1 in pigs appeared on ProMed over a week ago, but with dealing with swine flu up close and personal and all, I am only just getting to comment on it. This was a study done in the EU (VLA-Weybridge, Mammalian Influenza Group) to see how easy it was to infect pigs with the human-adapted swine flu, what kinds of symptoms and pathology it produced, and how transmissible it was. The answer seems to be easy, mild and very, in that order. 11 pigs were inoculated intranasally and when they began to shed virus a naive pair of pigs placed in…
There is no reason why a flu blogger-epidemiologist-physician's family should be immune to flu in the community. And it appears my family is not. My daughter has had a cough for the last few days and Friday night was suddenly seized by nausea, vomiting and fever. Her HMO's urgent care directed her to the Emergency Room of the local hospital where a rapid flu test was positive. While waiting to be seen at the ER, her 10 month old, who had a croupy cough, also started vomiting and was warm to the touch. His (slightly) older brother (2 years) was also coughing. Her husband has a cough, too, and…
Influenza 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…
At Friday's press briefing on the swine flu outbreak, Canadian Press's Helen Branswell twice asked whether CDC's weekly flu surveillance data showing the uptick in swine flu but also an unexpected prevalence in seasonal influenza was an artifact of increased testing or something new and unusual. CDC's Dan Jernigan was not especially clear, but seemed to acknowledge there was a lot of seasonal flu around: The CDC said part of the increase is certainly due to the fact that much more influenza testing is going on these days, because of concerns about swine flu. But the agency said it seems that…
Over 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…
Yesterday DemFromCT had another in his continuing series at DailyKos on Flu and You (Part VIII). He extended an earlier post (part II) on a critical piece of public health infrastructure, laboratory surveillance. One of the graphics is this chart of influenza positive tests reported to the CDC by the WHO/NREVSS collaborating laboratories: What you see in this chart is a weekly record of what seasonal influenza types and subtypes are circulating in the community (influenza A/H1N1, A/H3N2, B; swine flu makes a late appearance, far right). Flu seasons differ on dominant subtypes, whether they…
The spate of swine flu articles in The New England Journal of Medicine last week included an important "Perspective, The Signature Features of Influenza Pandemics — Implications for Policy," by Miller, Viboud, Baliska and Simonsen. These authors are familiar to flu watchers as experienced flu epidemiologists and analysts of archival and other data. Analysis of archival data is sometimes described as archeo-epidemiologic research. In their NEJM article Miller et al. summarize what they see as some common features in the three flu pandemics of the last century (so the generalization that there…
As I write this the US has 279 confirmed cases and one death from H1N1/2009 in 36 states. WHO has tallied 1085 1124 cases in 21 countries with 25 deaths. There is a backlog of samples waiting for confirmation, so by the time you read this the counters will probably have rolled upward, especially as state laboratories become facile with the new primers and are able to do their own confirmation. And predicting an increasing case count is about all anyone can say with certainty at this point. What we said once about flu pandemics can be said just as appropriately for the flu virus: "If you've…
There have been questions in the comments about where the CDC estimate of 36,000 to 40,000 influenza related deaths a year comes from. It's a figure I've used a number of times here to say generally that regular old seasonal influenza may be a mild disease for some but not for many others. Even if you don't die of flu, it can be a miserable illness and lay you low for several weeks of acute illness and months of fatigue and malaise. Now the 36,000 deaths number is taking on a life of its own, so it's time to explain exactly what it is and what it isn't. There are more things it isn't that it…
[NB: I have been traveling and offline all day. No way I can even read much less respond to the many excellent comments, tips, questions. Thanks to all. Help each other. Back at home base now.] Closing US borders with Mexico for swine flu is fruitless since the virus is already planted in a dozen or more countries. And while right wing xenophobes are trying to blame Mexican immigrants, most of the international spread has come from commercial travelers, either tourists or business people. If we had sealed the borders, would it have included all American nationals in Mexico? Somehow I don't…
Just a brief note to remind everyone about the case definitions CDC is using for reporting on swine flu (or whatever name we collectively settle on). In order to make sure numbers are comparable from day to day and place to place we have to decide on criteria for knowing we have something to count. Is someone with flu-like symptoms to be counted as a case? Or do we confine it to someone with laboratory proved infection with the virus? Should there be different categories of diagnostic certainty? For the moment, CDC is using the following definitions for suspected, probable and confirmed cases…
There were 3 flu pandemics in the 20th century and each has gotten an unofficial name. 1918 was the Spanish flu, so named because the Spanish were the only ones honest enough to acknowledge its presence initially and thus got stuck with the blame. Like the other two pandemic viruses it probably originated in southern China (although its history is cloudy), so the nicknames of the 1957 (Asian flu) and 1968 (Hong Kong flu) are probably more apt, or at least less inapt. Now we have swine flu. Excuse me. I mean influenza A/H1N1, since that is how WHO is calling it so as not to impugn the good…
A reader (hat tip, sandy) has pointed me to a very interesting interview with CDC's chief virologist, Ruben Donis, in Science Magazine's blog, ScienceInsider. In it he provides further information on the confusing reports about the species origin of the current swine flu, originally said to be of swine, human and bird origin but later claimed to be only swine. It may be that both are true, depending on how you look at it. According to Donis, who has been sequencing the isolates, the virus is all recent swine but bears the marks of human and avian ancestry in some genes. Different genes have…
There 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…
As 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…
One 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…
The 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…
Usually "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…