Since wild bird flu is front and center now, it is worth briefly reviewing why they are central.
Wild birds have always been key in influenza evolution.
Flu evolves via dual infections, which happens when one organism is infected by two viruses. The two viruses can exchange genetic information. In the case of flu, its 8 genes are a separate pieces of genetic information. The genetic exchange can be with whole genes (a new viruses take some genes from one parent and some from another) or pieces of genes (the new gene is a chimera with some input from each parent).
Swapping whole genes is pretty easy to see, and that is one thing that influenza analysts look for. Some think that H5N1 needs to get a whole human/pig gene to go pandemic. They have been watching and waiting, and helping WHO write its press releases announcing the latest H5N1 has no human genes, but that is not how H5N1 will go pandemic. It has never been reported to have gone that route, and there is no logical reason to think that reassortment is a requirement.
Swapping pieces of genes is harder to see. This happens via recombination, and although such a process is not new, its widespread role in evolution, especially from rapidly evolving viruses like avian flu, is not understood, and in fact is denied by those advising WHO and controlling information flow.
Thus, WHO doesn't talk about recombination because its advisors don't know how to recognize it, and if they do see it, the try to explain it by random mutation. However, the changes are far from random, and in fact can be traced back to genes of parental viruses.
Flu doesn't have time for random changes. To survive, it needs to change its genetic composition each year, and it does so via recombination, which requires dual infections.
Nature reserves offer an ideal environment for such an exchange and Qinghai Lake in China is a good example. Many species arrive at the same time from several geographically distinct region carrying distinct viruses. At the reserves, there are dual infections and the virus evolves. The birds then fly the virus back to areas where other indigenous viruses are and the virus evolves some more.
Most of these exchanges in the past where not easily seen, because there was not a good database of wild bird sequences, and much of the exchange involved wild bird sequences from serotypes like H9N2 mixing with H5N1, which were read as random mutations.
In May that changed because the H5N1 ar Qinghai Lake left a trail of dead bodies because it was killing wild waterfowl. The H5N1 was a clear recombinant, with parts of its genes from Europe, and parts from Asia. The HA cleavage site, which makes it pathogenic, was the characteristic KKKRRK, which was only found in H5N1 in Asia since 1996.
This signaled the beginning of a geographical expansion of H5N1. It was now in long range migratory birds, and can travel 1000 miles in a day. The H5N1 moved from Qinghai Lake to Chany Lake in Russia and also spread to neighboring Kazakhstan and Mongolia. Prior to July, Asian H5N1 had never been reported in any of the three countries.
Now H5N1 is entering Europe as the birds from Siberia migrate in. They have the same Asian H5N1 and signal the start of a global expansion outside of Asia. This will spread worldwide in the next 12 months.
This geographical expansion will allow the H5N1 to dually infect new organisms with new viruses, including mammalian ones in swine and humans. H5N1 will become more human like and achieve efficient transmission.
That is the problem. It is driven by recombination and will accelerate in the upcoming months. That's why the pandemic is a when, not an if, and why the when is measured in months, not years.
The pandemic is not dependent on random mutations or reassortment. It is driven by recombination, and H5N1 is collecting a lot of new toys to play with as it goes global.
...end of Dr. Niman's first posting....
Maybe you or someone else also knowledgeable can explain Mother Abigail's post and comment above. After reading Dr. Niman's article, my simpleminded brain says "how can they make a vaccine when it's not done recombining yet, but the article above it says that a vaccine is being made?"