Science Buddies: "Ask an Expert"

I really need some help with my project. At this website: http://www.flu.lanl.gov/vaccine/ there are a lot of flu raw DNA codes organized by northern hemispheres and southers hemisphere. If anyone knows a lot about this subject please help because I don't get it. When you get the code is it the vaccine or the virus. When you put the code into BLAST do the viruses or vaccines come up?

martonp,

The sequences you see are for the viruses only.

When mentioning using the viruses as vaccines; that usually means that the virus itself (capsid, coat, proteins, etc.) has been destroyed via heat treatment, protease treatment, or some other method. After debilitating the virus structure and components, the "dead" virus is injected into live mammals and the mammal reacts only to certain parts of the virus that are intact (known as epitopes) if at all. They key here is that the virus is unable to replicate and infect mammalian cells. Sometimes, mammalian immune systems will not react to any viral epitopes. Consequently, there are strong debates about how vaccinations should be done. Specifcally, some believe that giving a dead virus intact is the best way to vaccinate people. Others believe that analyzing viral genes and thus their resulting proteins and structures will elucidate what, if any, particular proteins or epitopes actually interact with mammalian immune systems; thus providing only this epitope will be the safest vaccine solution. However, both sides have their drawbacks. I probably wrote more than you wanted to know; but I hope some of this helps. Feel free to ask any questions you may have.

Best,

James

Thanks James,

OK, that answers a lot. But the project that I'm doing ( you can see the website address of my information bar) tells me that you can get the information on the vaccine and the virus. When you do the BLAST comparison, the matches between the raw DNA of the virus and the vaccine shows how many matches there are between the two and the more similar they arethe better the vaccine is because your immune system will be ready for that. So... where are the vaccine codes?

Thanks in advance,
Martonp

Martonp,

I think you just answered your own question. If you did a BLAST comparison with viral genome and the vaccine version of the virus, then don't you already have the "vaccine code?"

I just read your project summary. It looks like you have a handful to do. Is there a particular year, strain, and vaccine that you are currently analyzing? If you're just doing BLAST comparisons of the flu strains on the lanl.gov page, then you've pretty much answered your own question.

Best,

James