Flu viruses can be characterised in many different ways. One system uses types and subtypes. There are three “types”, A, B and C. Subtyping is based on two of the eight influenza genomic segments, hemagglutinin (H) and neuraminidase (N). Different versions of these two genes are designated with a number. For example: H5N1, H1N1 and H3N2 are three different subtypes of type A influenza. There are some important limitations to this system. Most importantly, two very different viruses may have the same subtype. For example, there is a “seasonal” H1N1 flu virus which is very different from the currently circulating “2009 pandemic” H1N1 virus. Further, the flu virus that caused devastating flu pandemic in 1918 was also subtyped H1N1, although it is significantly different from both “seasonal” H1N1 and “2009 pandemic” H1N1. This confusing situation arises because the subtyping system only reflects two of the eight flu genomic segments. Reassortment events can mix and match different genomic segments resulting in viruses that share some, but not all genomic segments in common. The only way to know whether or not a reassortment event has occurred is to sequence all eight genomic segments, not just the hemagglutinin and neuraminidase genes.
During the major outbreaks of 2009 pandemic H1N1 in the United States, “seasonal” H3N2 and H1N1 were almost entirely absent. There was some speculation that 2009 pandemic H1N1 would drive the “seasonal” flu viruses to extinction. This idea appears to be premature.
In Taiwan (Focus Taiwan, July 27, 2010), Singapore (asiaone, July 23, 2010) and Hong Kong (Center for Health Protection, July 17, 2010), 20%, 45% and 27% of all recently reported flu viruses were found to be H3, respectively.
There have been recent reports of H3 viruses in Iowa, Minnesota, Arkansas, Wisconsin, Pennsylvania, and Hawaii (Iowa Department of Public Health, July 30, 2010) [hat-tip, Pixie]. This has apparently led to the mass emailing of an Health Alert by the CDC advising doctors to be on the look out for H3N2 infections (CDC, August 4, 2010) [hat-tip, Goju]. The reason for this Advisory is unclear.
It is not clear whether all eight genomic segments in the viruses causing these outbreaks in Asia and the United States have been sequenced. Thus, we cannot know for sure that they are truly the “seasonal” H3N2. Dangerous reassortments between H3N2 and H5N1 have recently been reported in pigs in China (Bi et al. 2010). It is important to characterise flu viruses causing new outbreaks by sequencing all eight genomic segments. This is neither expensive nor technically difficult. However, it is not clear that the CDC has the necessary expertise to process samples rapidly. It is also not clear how rapidly a detection of a change in circulating flu viruses would be reported.
Bi Y, et al. (2010) Novel swine influenza virus reassortants in pigs, China. Emerg Infect Dis.