Surveillance
revere | November 10, 2009Nursing homes (Long Term Care Facilities, LTCFs) are a favorite hunting ground for respiratory viruses, including flu. They are open to the general community, where visitors and employees mingle freely with the residents. The residents are usually of an advanced age, have other sicknesses that make them vulnerable and often have less active immune defenses. So when the swine flu pandemic began at the end of April, the Public Health Laboratory at Ontario's Agency for Health Protection and Promotion ramped up their respiratory infection outbreak registration system with the prospect that LCTFs…
revere | November 6, 2009Helen Branswell, the Canadian Press's extraordinary flu reporter, is one of the few reporters who could have written the article, "Flu dogma being rewritten by a strange virus no one pegged to trigger a pandemic". She's been following flu for years and has watched as one thing after another we thought we knew about flu has been shown wrong -- by the flu virus. It's a theme we have been sounding as well for almost as long. As scientists we've seen one alleged flu truism after another was stood on its head. A couple of years ago we began to assume anything said about flu was provisional. Some…
revere | October 30, 2009One frequently hears claims that the current swine flu pandemic has been exaggerated because there are "only" 1000 or so deaths, while seasonal flu is estimated to contribute to tens of thousands of deaths a year. There are two reasons why this is not an apt comparison. We've discussed both here fairly often. The first is that the epidemiology of a pandemic and seasonal flu are very different. Epidemiology studies the patterns of disease in the population and swine flu is hitting -- and killing -- a very different demographic from seasonal flu. Its victims are young and many are vigorous and…
revere | October 22, 2009A reader (h/t MVD) sent me this link to a "CBS News Exclusive," Study Of State Results Finds H1N1 Not As Prevalent As Feared. As far as I can see the main aim was to raise CBS News's profile and gain readership. That's what news organizations do. We hope they do it by good journalism. I think this is an example where the reporters just didn't have enough knowledge of what they were reporting and put the wrong spin on it.
The central claim is that CDC stopped testing for swine flu hastily and without advance notice to the states:
If you've been diagnosed "probable" or "presumed" 2009 H1N1 or…
revere | October 19, 2009Monday morning, start of week three of the official flu season (which began October 4). CDC's scientific spokeswoman on the flu, Dr. Anne Schuchat has said we are seeing "unprecedented" flu activity for this time of year, including an unusual toll in the pediatric age group. What does "unprecedented" mean? It's not very specific on what precedents are included, but if we confine ourselves to the three years before this one, we can get a good idea of just how unusual this flu season is. This week CDC unveiled a new graphic for their Emerging Infections Program (EIP) (I liked the old one better…
revere | October 11, 2009If you are hesitating to be vaccinated for swine flu this year, perhaps this post will help you make up your mind. If it does, I hope it pushes you to get vaccinated, but whatever persuasion we attempt here will only be from a recital of what we know of the epidemiology of this pandemic. Because it is the different epidemiology that is the main feature, not the clinical characteristics or the virulence of the virus. So far this looks pretty much like a standard influenza A virus -- except for the epidemiology. Since I'm an epidemiologist, you might expect me to think this is important, and I…
revere | October 4, 2009This is about a paper published Friday. The post is long because the paper provides practical advice on a problem of importance, the issue of school closures. The advice is based on data and could be implemented at the level of a school district or even a single school without requiring a lot of money or effort. It's not cost free, but could probably be done with existing personnel and resources. The fact that it would be grounded in empirical evidence makes a decision to keep a school open or to close it much easier to defend. It would not be arbitrary or a guess. Improvements in the…
revere | September 28, 2009A good story by the AP's Lauran Neergaard yesterday highlighted the need for better public health surveillance and the efforts being made to improve it so as to keep track of possible rare side effects from the swine flu vaccine. This is an issue we've talked about a lot here, most recently in the context of not being able to fully test any vaccine for rare adverse outcomes prior to deployment. There's more involved than that, but first here's Neergaard's lede:
The U.S. government is starting an unprecedented system to track possible side effects as mass swine flu vaccinations begin next…
revere | September 27, 2009Flu season has started in earnest, even though it's not "officially" flu season until week 40 (first week in October this year). How do we know it's flu season if we don't test everyone and can't count flu? We use a surveillance system. The flu surveillance system has lots of moving parts and five or six components (or as many as nine, depending on how you count). None of them tell us exactly what we want and putting the different pieces together can sometimes be like the blind men and the elephant. But the system does work better than you'd think and it's undergoing modifications and…
revere | September 13, 2009At the beginning of September CDC initiated a new system for monitoring influenza activity. We reported last week that the old system ended on August 30 and that we were now into the new flu season. We even titled the post, "End of Flu Season." To paraphrase Mark Twain, the reports of the death of the 2008 - 2009 season may have been exaggerated. Well, not really, but the advent of the new system caused some confusion, at least for us, and we think we should clear it up.
There are several interconnected issues here. One is that the way trends in influenza will be monitored has been changed…
revere | September 10, 2009Flu season is over. Before you heave a sigh of relief, I'm talking about the (official) 2008 - 2009 flu season, which ended August 30 in week 34 or the calendar year. Welcome to the new flu season, the one called 2009 - 2010. It promises to be, well, "interesting."
Not that the one just concluded wasn't interesting. Indeed before we get done analyzing the data already collected it's likely to be the most informative in flu science history, partly because we have tools we never had before, partly because we have information gathering and handling capacity we never had before. But mostly…
revere | September 2, 2009Yesterday one of the questions we asked was whether swine H1N1 would replace seasonal viruses this season. In previous pandemics one subtype completely replaced its seasonal predecessor: in 1957 H2N2 replaced the H1N1 that had been coming back annually at least since 1918; only 11 years later, in 1968, a pandemic with H3N2 replaced the H2N2. H2N2 is no longer circulating but in 1977 an H1N1 returned and has been co-circulating with H3N2 since then. This was a new situation. We could ask why this hadn't happened before with H2N2 and H1N1 or H2N2 and H3N2 or all three together; or we could ask…
revere | August 9, 2009The other day we did something we don't like to do when talking about flu, we made a prediction. We predicted a bad swine flu season in the fall in the northern hemisphere. The history of flu epidemiology is that making predictions is dangerous. Flu has the ability to make fools out of anyone, regardless of expertise. One commenter in particular disdained the risk we took as being no risk at all. It was perfectly obvious to him (or "anyone paying attention") that next flu season would be a swine flu horror show. It may well be, and then this commenter will certainly gloat and perhaps have…
revere | July 27, 2009CDC's Advisory Committee on Immunization Practices (ACIP) recently rolled out their 2009 Recommendations. It's for seasonal flu, for which a vaccine exists, not for swine flu, for which there is (as yet) no vaccine. There is a lot to say on the subject of vaccines (see what we've said over the years under the vaccine category), but this seems like a good time to review some basic terminology, including what is meant by vaccine efficacy or effectiveness and how it is measured or estimated. There's a lot to say, so we'll split this into two posts, and in this one we'll go over some terms and…
revere | July 25, 2009Yesterday CDC announced it would no longer report confirmed and probable swine flu cases. This will likely cause consternation in some quarters, but the reasons make sense. First, it should be said that the real pressure to stop counting is coming from the states, where resources are stretched so thin and the value of the numbers so meager they no longer could afford to do it. The data, like most notifiable disease data, comes from state health departments, not the CDC itself. It is also recognition of what everyone knew from the earliest days of this outbreak: the "official" numbers did not…
revere | July 17, 2009Data from the Emerging Infections Program (EIP), one of the component parts of the CDC national influenza surveillance system, is showing that for some segments of its population the US did indeed experience a second flu season. The segment of particular concern are children between the ages of 5 to 17 years old, and to some extent adults between the ages of 18 and 49. The EIP counts only laboratory-confirmed hospitalizations in 60 counties located in 12 metropolitan areas in 10 states (if you are wondering, the 12 metro areas are San Francisco CA, Denver CO, New Haven CT, Atlanta GA,…
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 | June 27, 2009Early returns on what is happening in the southern hemisphere suggest that novel H1N1 is crowding out the expected seasonal strains, something that pandemic strains have usually done. In 1918 there was a pandemic with the H1N1 subtype that settled down as the dominant seasonal flu virus until the "Asian flu" pandemic of 1957 when it was bumped by H2N2. That subtype ruled the seasonal flu roost for only 9 years when a new subtype, H3N2 took its place in the Hong Kong flu pandemic of 1968. Both pandemics were much less severe than 1918 but still resulted in millions of excess deaths globally.…
revere | June 25, 2009A story in yesterday's New York Times was headlined: In New Theory, Swine Flu Started in Asia, Not Mexico. That sounded pretty interesting. What's the new evidence? The answer? None. Just speculation. So what's going on?
Contrary to the popular assumption that the new swine flu pandemic arose on factory farms in Mexico, federal agriculture officials now believe that it most likely emerged in pigs in Asia, but then traveled to North America in a human.
But they emphasized that there was no way to prove their theory and only sketchy data underpinning it.
There is no evidence that this new virus…
revere | June 23, 2009CDC has another snapshot of what the flu surveillance system is seeing up through week 23 (ending June 13). It shows flu still circulating in many communities at a time when most seasonal flu is normally at a very low level. Indeed of the 2765 specimens tested in CDC's network of 150 laboratories, virtually all of the roughly 40% were influenza A (seasonal influenza B has all but disappeared; the others were not influenza). Not all the flu A viruses were or could be subtyped, but of those that were or could be, 98% were novel H1N1. IN other words, there's lots of flu around, but essentially…