BLASTing Flu Viruses

[billiegoat]

Hello,
I am attempting to do this project "BLASTing Flu Viruses", which can be found at https://www.sciencebuddies.org/science- ... p003.shtml.
After comparing many common virus strains to the same type of virus that was included in a vaccine for specific influenza seasons, I found out that most of them were 90% or more (with the exception of two 80%~85%) identical. Since the flu virus wasn't included in the vaccine, I thought it would be less identical and more distinctive. For instance, 43% would make more sense than 97%. Please let me know if I'm using BLAST wrong or I did a step wrong. The high percentages of identical virus strains (for a common strain and the same type of virus that was included in the vaccine) don't make a lot of sense for me. Thanks y'all in advance.

[deleted-132180]

Hello there,

I'm not an expert on influenza genetics, but I'll try the best I could to explain this. Other experts, if you have any other ideas or if I explain anything incorrectly, please chime in!

If I'm reading the procedures for this project correctly, you're only comparing the sequences of two proteins from the different flu strains: hemagglutinin (HA) and neuraminidase (NA). These proteins are present in an outer protein coat called the viral capsid that encase the influenza virus genome. Because these proteins are present on the outer coat of the virus, they can be recognized and detected by the host immune system. This elicits an immune response and the generation of host antibodies that can recognize these viral proteins, and this is of course one of the most important aspects of the flu vaccine. There are at least 16 different HA subtypes and 9 different NA subtypes (more could have been discovered),and the HA and NA subtype of each individual strain is always included in the strain name (for example, H1N1 means the flu virus has HA subtype 1 and NA subtype 1). Because many different HA and NA subtypes exist, the human immune system is often challenged with new antigens if they are infected with a flu strain that had different subtypes from a previous strain that infected them. I don't know the exact mutation rate of influenza viruses, but often, point mutations occur in the HA and NA genes, leading to slight changes in the amino acid sequence or perhaps structural conformation of the proteins. This allows the virus to infect people who were either infected or vaccinated with a previously circulating virus since the proteins/antigens are different enough from what they've seen previously. However, the virus cannot change the amino acid sequence and structural conformation of these proteins TOO drastically either because these proteins are extremely important in interacting with host proteins to go through the viral life cycle. If the viruses change the HA and NA proteins too much, they may no longer be able to interact with their host receptors in the same manner and hence cannot go through their life cycle properly. Hence, it would make sense that the viruses only make small changes at a time to these proteins, so it's not too surprising if you see that the proteins are about 80-90% identical to each other. If two HA proteins are 43% identical to each other, one of them may have changed way too much to the point where it cannot bind its host targets anymore. Flu experts, correct me if I'm wrong!

I hope that answers your question. Let me know if anything I said was confusing or if you have more questions. Here are some links that may provide you with more information about the flu:

This page gives some really good info on the genetics of flu viruses: http://www.nature.com/scitable/topicpag ... -virus-716#

This page gives some really good info on how strains are selected each year to be put into the flu vaccine: http://www.cdc.gov/flu/professionals/va ... irusqa.htm

Connie

[billiegoat]

Hello Connie,

Thank you for the rapid reply! Your answer was extremely clear. Now I understand that the viruses only made minor changes because a drastical change can result in the virus unable to go through the host's receptors. Again, thank you for the quick and thorough answer.

-billiegoat