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Pastimes : SARS - what next? -- Ignore unavailable to you. Want to Upgrade?

To: Maurice Winn who wrote (929)	11/24/2004 4:57:15 AM
From: Henry Niman	Respond to of 1070

>>Why do they need to do it?<< There are some reasons for doing, especially if the experiment is done correctly. However, I don't think it will be, and consequently there will be no pandemic strain, just a lot of head scratching followed by hand waving, which is essentially what is happening now. The experiment is designed to eliminate the head scratching and hand waving. It won't, but it may lead to the correct experiment, which would prove that pandemic strains evolve from recombinantion, not reassortment. Right now the experiments are designed to see what combination of reassorted genes lead to a pandemic strain, so they will simply be reshuffling genes. The virus however takes advantage of reshuffled genes to make new genes, but it changes all 8 genes and then uses some natural selection to come up with the best combination. My guess is the experiment will only do one gene at a time and won't allow for recombination, so it will just be garbage in, garbage out because the experiment is fundamentally flawed. In science (and just about everything), you have to ask the right question to get the right answer, and as far as I can tell, these experiments are asking the wrong question. They are asking what combination of old genes makes a pandemic strain, instead of what new genes are formed. The virus clearly focuses on making new genes, which is why you need a new flu shot each year. But this is explained with hand waving (mutations due to copy errors), which is clearly wrong.

To: Maurice Winn who wrote (929)	11/24/2004 6:07:39 AM
From: Henry Niman	Respond to of 1070

Mq, I have posted more details on recombination and how it leads to species jumping recombinomics.com

To: Maurice Winn who wrote (929)	11/24/2004 7:40:22 AM
From: Henry Niman	Read Replies (3) \| Respond to of 1070

Here's a brief explanation of the differences between reassortment and recombination: Both reassortment and recombination have been known for some time, but most who study influenza don't realize that the chief driver of rapid evolution is recombination, which is why the concept is a paradigm shift recombinomics.com and the concept and applications are very patentable recombinomics.com Here is a quick summary. Re-assortment just re-shuffles genes. The flu virus has 8 genes and if two viruses infect the same cell, when the genes are package up there can be re-shuffling so gene 1 comes from virus A while gene 2 comes from virus B, etc. Thus the emerging virus has a new combination of genes. This can be seen in the serotypes, which just use 2 of the 8 genes. Thus, H3N2, H5N2, H7N2, H9N2 are 4 distinct serotypes. All have N2 but it is packaged with 4 different H genes to represent these 4 serotpes. Although all 4 N2s are closer to each other than to N1s, they really have some differences. Most influenza virologists would say the N2s are different because they mutated, but those virologists would be wrong. The N2s are different because when two viruses infect the same cell not only can the genes reassort, but they can also recombine. That happens when the gene copying machinery starts copying gene 1 from virus A and then finishes copying gene1 from virus B. In that case gene 1 is a NEW gene (its a chimera between the two gene 1s of the two viruses). The copying enzymes (polymerase) can actually hop back and forth many times (the process is called homologous recombination), and each time they create a NEW gene (and they can actually do this for all 8 genes creating 8 new genes). That's what viruses do. The evolve by quickly making new genes. That's what the 1918 pandemic virus did. That's what the H5N1 virus in Asia did. That's what the next pandemic virus will do. That's NOT what WHO and the CDC are looking for. They are looking for reassortments and can't figure out why they can't find them (while the virus is recombining every season).