With CDC Seasonal Flu Data Unavailable, An Electronic Medical Record Offers a Glimpse of Early Activity Levels

As Washington remains deadlocked on the implementation of the Affordable Care Act, the US government’s shutdown has resulted in the furlough of nearly 70% of the Centers for Disease Control‘s (CDC’s) workforce. CDC Director Tom Frieden recently shared his thoughts in a tweet. We agree whole-heartedly.  Although it’s all too easy to take the CDC staff for granted, they are the frontline sentinels (and the gold standard) for monitoring disease outbreaks.  Their ramp-down could have serious public health consequences.

We are particularly concerned about the apparent temporary discontinuation of the CDC’s flu surveillance program, which normally provides weekly reports on flu activity. Although flu season typically begins in late fall, outbreaks have occurred earlier in previous years. In 2009, flu cases started accumulating in late summer/early fall.  And given the potential for unique variants, such as the swine or avian flu, every season is unpredictable, making the need for regular CDC flu reports essential. We therefore hope to see the CDC restored to full capacity as soon as possible.

In the meantime, we would like to help by sharing data we have on communicable diseases, starting with the flu.

Because the athenahealth database is built on a single-instance, cloud-based architecture, we have the ability to report data in real time. As we have described in earlier posts, the physicians we serve are dispersed around the country with good statistical representation across practice types and sizes.


To get a read on influenza vaccination rates so far this season, we looked at more than two million patients who visited a primary care provider between August 1 and September 28, 2013 (Figure 1).  We did not include data on vaccinations provided at retail clinics, schools or workplaces.

This year’s rates are trending in parallel to rates over the last four years, and slightly below those of the 2012-2013 season. However, immunizations accelerate when the CDC, and consequently the media, announce disease outbreaks and mount public awareness campaigns.

As for the government shutdown, nearly everyone hopes for a quick end.  Should the standoff drag on, detection of the flu (or other diseases) may be delayed, in theory endangering the public. Fortunately, we currently see no evidence of an early influenza outbreak.  But recent history shows that the flu can begin spreading at any time, and once it does begin, it spreads very quickly, as shown in Figure 2.

We believe that our data provides a reliable view of seasonal flu trends. Last year, we wrote about the 2012-2013 flu season and found that patterns in our patient population (consisting of a large proportion of patients receiving immunizations in primary care settings) closely mirrored CDC trends. With that in mind, we believe that sharing our 2013-2014 data would be valuable to the health care community.

Whether our nation’s politicians can come to an agreement tomorrow or next month, we will continue to deliver reports that monitor population health and look ahead to contributing any information we can. If you have any suggestions or comments – on the flu or other diseases where up-to-date data would be valuable – please leave a comment here or e-mail me directly at isung@athenahealth.com.

Iyue Sung is the Director of Core Analytics at athenahealth. The post originally appeared on the athenahealth blog.

8 replies »

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  2. Hi m13,

    Thanks for your thoughtful comments and questions. To your questions:

    1. By “single instance, cloud base”, we mean that all of our clients accesses our software through their web-browser (cloud-based), so they are all using the same version (single instance). An analogy would be doing online banking via the web, on your computer; everyone would be using the same application. What this also means is all of our data sits in one (large) database, which allows us to do analyses across all of our clients, to uncover national trends.

    2. We have clients in 49 states, though of course, we’re concentrated more in certain states than others. We did not do any weighting or statistical adjustments. We found that in our estimates last year for the flu, overall patterns were similar to the CDC. You can see that in a blog post from earlier this year:


    3. As for comparisons to the CDC, here is a link to another blog post discussing vaccination rates:


    Thanks again for your comment and please stay tuned for our next post!


  3. Hi John,
    Matt Nix from athenahealth here. Thank you for your questions! We are looking at flu diagnosis and vaccination data for PCP visits on athenahealth’s network, and we have seen our trends track very closely to the CDC’s. Check out our blog later this week for more details on how well our data tracks.
    While the CDC furlough continues, we plan to release this data on athenahealth’s blog each week: http://www.athenahealth.com/blog/category/analytics-research/

  4. Iyue, very interesting data and great use of the analytics core of your work at Athena.

    Few questions about the methodology –

    1. What is the distinction between ‘single instance, cloud based’ architecture vs other means of data assessment?

    2. Do you have a density map to show the approximate distribution of Athena’s providers (I’m envisioning something like the 4G coverage maps that Verizon and AT&T are always showing) – are your providers really giving a fairly accurate statistical sampling of the country or are there clusters unaccounted?

    3. Do you have any data comparing Athena’s vaccination charts as compared with those from the CDC for prior years (ie are you fairly reflective of the broader picture).

    It’s very powerful to have publicly available information, in real time, from private entities that can provide some of the services that we expect from our public services. I wonder if we could use THCB and other forums to provide the other side of the CDC’s work, which is to educate and shape public behavior.

  5. Excellent contribution.

    On one hand, the shutdown-related restricted availability of influenza surveillance data should not influence our general recommendations that everybody get immunized barring contraindications.

    On the other, it certainly would be horrible if there was an earlier- or larger-than-expected flu season in need of special intervention at a time when the public health infrastructure is both blinded and paralyzed by the shutdown. I’m sure the truthy zealots in Congress would blame Obama for the deaths that would ensue even as they contributed to them with their shutdown.

    Many thanks,
    Tim Lahey
    ID doc & clinical ethicist
    Dartmouth-Hitchcock Medical Center
    Geisel School of Medicine at Dartmouth

  6. Interesting blog. Knowing vaccination coverage is interesting and I wonder if the graph depicting proportion of patients with flu are presumptive diagnoses are laboratory confirmed.

    Either way, CDC’s forced hiatus requires each of us and our organizations to don our prevention hats and educate patients and our communities about flu prevention, particularly the need for vaccination. This video was highlights some of our challenges in this area:

  7. I think this is a very cool idea. A quick question about methodology and your approach. The vaccination demand = indicator of activity argument sounds like a good way to keep an eye on what’s going but there will be people who wonder if you’ll be able to pick up a rapidly spreading influenza, the kind that really worries people who know how much damage a serious flu season can do. I assume you looked at the historical numbers and matched up vaccination rates and activity levels in previous flu seasons. Can you tell us a little bit about what you found?

    And second question – which is the important one – how and how often do you plan to make this data available to the public?