An influenza primer, updated for 2012/13

Enlarge / A schematic of the flu virus, with the H and N proteins shown on the surface in red and blue.

http://www.cdc.gov/flu/images.htm

2012/13 flu update: We're re-running the primer on flu biology (reproduced in full below) that we developed for the 2009 pandemic in order to keep you up-to-date with what's turning out to be a busy flu season. The fraction of people visiting physicians for flu-like symptoms rose from 2.8 percent to 5.6 percent during the last few weeks of 2012, according to statistics from the CDC. Since then, it seems to have started to decline.

At its peak, while this year was below some recent years (in the 2009 pandemic, that rate was 7.7 percent), that number still represents a lot of sick people. And, unfortunately, it represents fatalities. So far, the CDC has been made aware of 40 pediatric deaths from influenza this season, and that number is likely to rise over the coming weeks. Rates of hospitalization peaked at about 8.1 per 100,000 people.

The majority of people seem to be infected with the influenza A species of flu virus (although some influenza B is also circulating), predominantly H3N2—for more on that nomenclature, see below. The good news for those who haven't been infected yet is the majority of the viruses the CDC has seen are covered by this year's vaccine. So, if you got a shot, chances are good that you'll be protected.

Our original coverage follows:

Swine flu, bird flu, H1N1—tracking the influenza virus can be a confusing task, not generally made easier by the fact most people only attempt to do so when addled by flu symptoms or in the midst of worries about a potential pandemic. We recognize the latter appears to apply to the current situation, but we'll do our part to try to explain a bit of the biology of the virus. Putting together this explanation was made a bit challenging by the fact that anyone we could find who has detailed knowledge of the influenza virus appears to be busy actually working on the current outbreak.

On the surface: the HxNx nomenclature

Like most viruses, a spreading swine flu virus has a coat formed of proteins which surround the genetic material that allows the virus to hijack a cell and reproduce. These coat proteins are critical in a variety of ways: they determine which cells the virus can latch onto and infect and, being exposed, they're the things antibodies recognize when your body generates an immune response to the virus. For the flu virus, the major coat proteins are called hemagglutinin and neuraminidase—the H and N of the commonly used nomenclature for identifying these viruses.

Given the large and diverse flu virus population, there are many variants of each of these two proteins, but they fall roughly into a limited number of classes: according to the CDC, there are 16 known hemagglutinin classes, and nine of the neuraminidase. As such, it's possible to identify categories of viruses based on their specific combination of these two genes, leading to the typical nomenclature that we see in press reports about influenza: H1N1, H3N2, etc.