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The rapid evolution indicates the virus has run out of easy targets (those with no immunity) and now has to find changes that will allow for new infections. Researchers in Beijing deposted sequences from eight isolates from Beijing, which were collected in November.
http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.htmlThe sequences from all 8 were released for two genes, but those genes didn't have any changes. The NP gene however was present for 5 isolates and had a number of changes and these changes were in all 5 Beijing sequences, showing that the same evolving virus had infected many individuals in Beijing. The travel logs show which other viruses in the database have those changes, and there was quite a mixture, showing that the gene was picking up changes (largely from other H1N1's) via recombination.
However, the rapid evolution that will have the biggest impact is in HA, becasue that is were most of the immune response is, including the vaccine. Previously, the H1N1 has been evolvingly slowly becasue the virus could infect almost everyone (only those over 65 had significant immunity). These rapid changes however, are designed to defeat the immune response, including the vaccine. The number of changes were high and concentrated around the HA cleavage site. So far there are only 3 HA sequences, but many of the changes are found in 2 or 3 of the sequences, indicating the changes are real. The source of the changes is unclear, but since H1N1 can infect MANY species, the flu genes may be comg from species which are not well represented in the data base.
The bottom line however, is that the virus is now going to show how it can adapt and defeat current immunity. It is something that the virus does well, and a swine virus in humans that can infect many species is likley to result in quite a display, which will be a good show, but not a good result for hosts.
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