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EM - The end of flu season

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  • EM - The end of flu season

    Flu 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 because this was the season of the long awaited periodic influenza pandemic that history told us was bound to come. We just didn't expect that particular strain, subtype or starting location. Which is just what we did expect with flu. It always confounds us.

    We started with a more or less convention, if somewhat less severe, flu season with the usual seasonal H1N1, H3N2 and influenza B. One reason it seemed less severe was that this was mainly an H1N1 seasonal flu. Experience shows that H1N1 seasons are often produces less excess mortality, so when the season wound down in April it looks the influenza impact might not have been as bad as it sometimes is. Then the pandemic hammer fell and it fell with surprising swiftness, considering influenza virus doesn't usually like the spring and summer. From April to the end of August a new form of H1N1, this one of swine origin, added 40,000 confirmed or suspected cases to the official rolls, but everyone acknowledges these are just the tip of the iceberg. How much of the tip we don't know. CDC reckoned at one point over a million cases, too many to confirm or even count. It's just a guess. There were about 9000 hospitalizations and 600 deaths. Those are the officially recorded numbers, but once again, they are an underestimate, although not as much of an underestimate as the case count. It's obviously much easier to miss or ignore community cases than those severe enough to require hospitalization or resulting in a fatal outcome. But we have certainly missed hospitalized and fatal cases resulting from flu, so those numbers are the bare minimum.

    If we look at the surveillance system for the last flu season we clearly see we had two flu seasons packed into one. Here is a bar graph for positive specimens submitted to the 150 CDC/WHO labs involved in virologic surveillance in the US. You can clearly see the two components, the one on the left being the usual seasonal flu season, the one to the right (starting in week 17), the pandemic flu component. When interpreting this graph it is important to understand it does not represent what epidemiologists would call the "epidemic curve," the evolution of number of cases over time. That's because what is being counted here are the number of positive specimens for influenza of various types and subtypes submitted to laboratories, not the number of cases. If the fraction of all cases that were swabbed and submitted to these labs remained the same throughout the year, this could be interpreted as an epidemic curve, but that is not the case. The fraction changes continually as participating hospitals and practitioners change the way they take specimens, triage cases and submit samples from cases they suspect might be flu. But by looking at the colors of the bars one sees very clearly the two components. During the pandemic phase, the seasonal flu types (A or B) and subtypes and strains (seasonal H1N1 and H3N2 versus swine flu H1N1) change dramatically and become essentially all swine flu. So that tells us that many new cases appeared that were different (all the charts are from the weekly CDC surveillance report, FluView).

    We can see the same thing with pediatric mortality. This is (thankfully) much rarer and more accurately counted. Each year somwhere between 50 and 150 children die of flu, the higher figures being for really bad flu years.

    This year we will end up with something like 111, but over a third (43) were swine flu deaths. Without them this season would have had fewer pediatric deaths than last season, which was a comparatively bad flu season. The double hump in pediatric deaths in the 2008 - 2009 is plainly different than the pattern of the last three years.
    The results of the pandemic are harder to see but still visible in another major component of the surveillance system, the 122 city count of pneumonia and influenza (P&I) deaths. You need to know how to read this graph to see the evidence of the pandemic in it. Deaths from P&I vary seasonally. Not all of them, or perhaps even most of them, are from influenza. There are a lot of other respiratory viruses and other things that cause pneumonia than viruses. You can see the seasonal average as the bottom wave like solid line. Since that's an average (obtained from data over many seasons but taking variation in year to year seasons into account), the actual number of P&I deaths each week vary around that bottom solid line, sometimes above it, sometimes below it. When influenza goes through its seasonal cycle it adds to the P&I death total. The upper solid line is also a statistical average, this time the one representing the upper 35% or so of seasonal variation. When there is a lot of flu around it pushes P&I deaths into that upper zone (above the upper solid line). Those are the excess deaths associated with flu season. For seasonal flu, those are mainly people over the age of 65. You can see that this occurred for a few weeks around New Year in the 2005 2006 season, but that the 2007 - 2008 was a fairly bad year, contributing a lot of excess mortality (we covered all this in detail in a previous post, "How do we know how many people die of flu every year"). It is the excess deaths, the ones poking above the upper line, that represent the oft misquoted figure of 36,000 deaths from seasonal flu each year. As you can see, for four of the last five years this number was essentially zero (essentially nothing poking above the line). But many years the numbers are more like 2007 - 2008, sometimes seventy or eighty thousand. On average they amount about 36,000 over 20 or so flu seasons. This year, except for a week or two in May or June (it's hard to tell from the graph), it was again very small. So how do we see the evidence of the pandemic? This year looks much like the other years except for the bad one of 2007 - 2008:
    But if you look more closely you will see something else. Starting at week 20 P&I deaths are above the seasonal average every week. The only other time this happened over this spring summer stretch was in the bad year of 2007 - 2008. In that case these were mostly the elderly. This year, they are mostly in the under 60 age group. That's one of the reasons the effects aren't so evident in the P&I graph. Most of the seasonal average P&I mortality is in the elderly and the noise from that age group is masking the pandemic effect.

    You can see the age effect most clearly in another series of charts. In each of the panels, from top (the youngest) to the bottom (the elderly) you will see a dashed line. That's the seasonal average rate of flu per 100,000 population. These numbers are cumulative, so as the weeks go on the curve has to rise (each week adds to the week before). When the line reaches the dashed line it means that we have reached the point where the risk to an individual of getting flu is equal to the average risk of the last three years during the months considered "flu season" (October to April). Flu season peaks in January to March depending on the year. Your risk of getting flu "off season" (April to October) is very low (as far as we know, although we haven't done very much surveillance in this time period so that may be a statement that will be revised in coming years). But the way the graph should work is that the line starts at zero at the beginning of April or May (here it is week 16, sometime in April I think) and if it is an "average year" it should reach the dotted line by the following April. But you can see that for some age groups things are already ramping up.
    But if you compare the 65+ panel (bottom) with the 5 - 17 year old age group you'll see a dramatic difference. For the oldest age group the flu season is just starting (note that the vertical scale differs for this this age group). It is just barely inching up from the bottom. But in the age group hardest hit by swine flu, 5 - 17 year old, the risk of flu has already exceeded the seasonal average for the end of the flu season and we're not even to October. We're already there for adults (18 - 49 year olds), too. And the risk for the under 4 year olds is on the way. Getting old stinks (I know), but in this case I'm doing better than a 4 year old. It's something, and I'll take it.

    Finally, if you have any doubt that the new flu season is now underway, take a look at the percentage of outpatient visits for influenza-like illness (ILI) to the CDC network of providers that are part of ILInet. Not only has that percentage been higher than the previous years, but there is now a marked uptick.
    The 2008 - 2009 flu season is over. The 2009 - 2010 flu season is here. I'm not going to say, "Welcome."

  • #2
    Re: EM - The end of flu season

    Wow, I can't tell you enough how informative this is. Thank you so much!


    • #3
      Re: EM - The end of flu season

      "End of flu season" redux

      Category: CDC Epidemiology Infectious disease Surveillance Swine flu
      Posted on: September 13, 2009 1:26 PM, by revere

      At 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 and the changes reflected in the FluView report issue Friday (September 11). The change affects an important part of a multicomponent surveillance system, but it is not the only part, the one that counts influenza and pneumonia deaths and now hospitalizations. The previous counts will be reset to zero and new counting began this week. But there are another 8 or 9 components to the existing influenza surveillance system that has been in place for decades and administratively extended starting from week 40 (October) of the fall in the northern hemisphere to week 20 (April) of the following spring. This is only part of a year but was considered "flu season." This year the normal surveillance continued throughout the spring and summer because of the advent of the 2009 swine flu pandemic in April. I hope that we will be seeing year round surveillance from now on. Still, because of decades of data, CDC is retaining the October start date for the 2009 - 2010 flu season, even though they acknowledge it looks like the actual flu season may already have started. The reason for this is to allow consistent comparisons.

      So a new flu year has indeed started "on the ground" and state reported flu hospitalizations and deaths have been reset to zero. So the idea that the new flu season has begun is correct. But in an administrative sense CDC is retaining week 40 as the start of the 2009 - 2010 flu season (and Sept. 30 as the end of the 2008 - 2009 season), so in that sense we were premature in reporting "the end of flu season."

      These may seem like arcane points of administratrivia, but they are very important to those trying to figure out what is going on. The new state reporting system for influenza and pneumonia hospitalizations and deaths has two sources: laboratory confirmed hospitalizations and deaths from influenza reported to state epidemiologists by hospitals; and hospitalizations and deaths from pneumonia and influenza reported to state epidemiologists. The latter are clinically defined and include all types and subtypes of influenza (i.e., both flu A, seasonal and pandemic and flu B but also deaths that are not clinically distinguishable from an influenza pneumonia caused death even though there is no laboratory evidence to corroborate it and will have been caused by something else. Prior to the pandemic state epidemiologist did not provide weekly reports of all hospitalizations and deaths from pneumonia and influenza, but began to do so specifically for confirmed and probable cases of A/swine flu 2009 when the pandemic started in the spring. That system has now been formalized and all influenza and influenza like pneumonia and flu hospitalization deaths added to the surveillance system. Thus the new system that just started is a continuation of one that started with the pandemic but enlarged to include all pneumonia and influenza hospitalizations and deaths each week as reported by each state's epidemiologist in charge of CDC notifications (typically two per state).

      Here is CDC's rationale for broadening the system beyond the pandemic strain, indeed beyond influenza. As an epidemiologist I see it as a compromise, but one that makes sense. It is not the only one that could have been made, but I consider it highly defensible:
      CDC believes that regular seasonal influenza viruses will co-circulate with 2009 H1N1 influenza and capturing all laboratory-confirmed influenza will provide a fuller picture of the burden of all flu during the pandemic. There are too many cases of flu to test and confirm so laboratory-confirmed data is a vast underestimate of the true number of cases and this bias would be exacerbated over the course of the pandemic as more and more people become ill.
      Influenza and pneumonia syndrome is a diagnostic code used by all hospitals. Capturing this number will reflect a fuller picture of influenza and influenza-related serious illness and deaths in the United States during the pandemic. Influenza and pneumonia syndrome hospitalizations and deaths may be an overestimate of actual number of flu-related hospitalizations and deaths, but CDC believes influenza and pneumonia syndromic reports are likely to be a more sensitive measure of flu-associated hospitalizations and deaths than laboratory confirmed reports during this pandemic.
      The rest of the influenza surveillance system will continue as before and will have its numbers reset October 4, not September 1. If this seems a bit confusing, it is. It will get sorted out over time, I expect, but right now it seems a bit discordant. There are good reasons for each decision, but the net result seems a bit like what the computer people call a kludge. Within the regular system there is a laboratory virologic surveillance component involving 150 laboratories (that includes all the state labs). This system will continue to keep track of what types and subtypes of influenza are being seen in clinical laboratories. This means that lumping all the pneumonia and influenza hospitalizations and deaths in the state reports won't result in a loss of that information because it will continue to be available through the existing system. In addition, the percentage of total deaths from pneumonia and influenza deaths in the network of 122 cities will continue as before, using the same definitions, allowing a comparison to the new state reporting system with what we've been seeing in years past by other means. Similarly, the network of physicians who report the proportion of their visits for influenza-like illness (ILI) each week (so-called ILI-Net system) will remain. It is this system which seems to show that the new flu season has started in earnest, with the proportion of ILI visits up considerably from what we would expect at baseline. CDC usually waits for this to happen three weeks in a row before calling a flu outbreak, but that seems certain to happen within the next week or two. So we're really there, and it's only the first week in September. In other words, it looks like we are having a very early flu season. That could mean it will also end early or that it will smoulder along all year or that it will get really bad.
      Because this is flu and you never know what it will do.

      You can read the gory details about the "new" system here. Here's the ILI-Net for the week. Disentangling the signal from the noise isn't too hard:
      Source: FluView, September 11, 2009