and my whole science fair writeup (excluding graph and title):
What is influenza?
Influenza, or the flu for short, is a contagious respiratory infection. A tiny virus that can spread through an infected person’s body, causing coughs and sneezes, causes the flu. The flu causes fever, headache, sore throats, body aches, sneezing, coughing, sensitivity to light, and fatigue. The infection attacks nasal passages and lungs. The flu season is from late fall to early spring. “Flu seasons” refers to the period of time in which flu outbreaks are common. Contrary to popular belief, the flu is not just a worse version of the common cold. The common cold doesn’t have complications involved with the flu, usually pneumonia. The two viruses aren’t even distantly related. The flu virus looks like a ball with two types of spikes coming out of it.
What are some of the characteristics of different types of flu?
There are three main types of the flu, types A, B and C. Type A is the most serious, because it can infect both humans and animals. Type A is usually the type that causes global pandemics. Type B is also a major concern, as it mostly affects children and causes them to be absent from school. It has also become resistant to major antiviral medications in Asia. However, Type B flu is contained in humans only. Type C is less severe than its counterparts Type A and Type B. It can cause outbreaks, though less serious than those caused by the other types. Type C is the most like the common cold, and protection against it is not in the annual vaccine because it is so mild compared with the other two.
How are strains of the flu named?
First, the strains of the flu are sorted by their type: A, B, or C. Then they tell you where it came from. This is where the strain was first isolated. Next, there is a number indicating the number of viruses isolated in that certain year and location. Then, the strain’s name tells the year it was isolated. After that, they tell you the specific surface proteins (hemagglutinin and neuraminidase). There are 15 hemagglutinin proteins, but only 3 occur in human influenza. In human influenza, there are 3 neuraminidase proteins out of the 9 total. All hemagglutinin and neuraminidase proteins are associated with avian flu.
Why is the swine flu such a big deal?
Flu viruses are coated with proteins that attack our receptor molecules on the outer surfaces of our cells. These molecules bind, and help the virus force our cells to make viral proteins and genes. In the flu, the proteins overpowering our cells are called hemagglutinin (HA) and neuraminidase (NA). In abbreviation, these are H and N proteins with numbers that show an antibody response to them. For this reason, they’re also called antigens. Antigens help to figure out how flu strains will affect humans or animals.
Some strains of the flu have antigens bind two different animal hosts, with one being closer to humans. This host has antigens related to flu strains in both birds and humans. For the swine flu, the host that was closer to humans was swine, and the other host was avian. Pig cells are lined with receptors that could allow both human and avian strains of flu. By chance, a pig was infected with bird and human flu at the same time, and both viruses were present in one of its cells, the viruses could easily mix genes inside the cell to create new flu strains, able to infecting humans and birds. Once the avian flu passed to swine it could easily be transmitted to humans and reach pandemic levels.
What is a mutation?
A mutation is a change of a gene’s normal sequence. They are caused by environmental factors or mistakes made while the gene was being copied. Mutations in surface protein genes allow viruses to remain infectious year after year.
How are vaccines made?
The process by which vaccines are made is long and requires an unbelievable amount of fertilized chicken eggs. (This process has gone through only a few changes since its development in the 1940s, although health officials complain about the time-consuming processes.) Currently, it takes 6 months and more than 100 million hen eggs to create seasonal flu vaccines. Apart from this, viral surveillance need time to figure out which viruses need a vaccination against.
First, viral samples from people who are sick with the flu from various parts of the world are collected. Viruses to be in the vaccine are decided by the World Health Organization (WHO). While this is happening, vaccine manufacturers buy millions of eggs for the influenza vaccine. The Food and Drug Administration (FDA) prepares the viral samples collected for use in vaccines. The viral preparation goes into the fluid around the chick embryo eleven days after the egg has been fertilized. The embryos are infected, and after being incubated for a week. Then the viral material is deactivated and purified.
What is the objective of this experiment?
The objective of this experiment is to see whether flu viruses from different seasons mutate at the same regions of protein. If a single protein is mutating between strains, then the protein can make the virus more contagious and therefore possibly more resistant to vaccines. If a set of proteins is simultaneously mutating between strains, then the information gathered will not be as clear.
1) Go to the Flu Activity & Surveillance page at The U.S. Centers for Disease Control and Prevention (CDC) website:
www.cdc.gov/flu/weekly/fluactivity.htm.
2) Click on "Go" next to the year 2008-2009 “Current Weekly Influenza Report”.
3) Read the information on the page. In particular, find the paragraph with the heading "Antigenic Characterization." It will tell you the name of the virus strains prevalent in this year.
4) You can obtain the sequences for these strains from the NCBI GenBank website:
www.ncbi.nlm.nih.gov/Genbank/.
5) Select "Protein" with the “Search” drop-down menu. Type in the name of the flu strain (use A/California/07/2009 (H1N1) in the search box.
6) Full-length HA is 566 amino acids. In order to retrieve full length-entries, add this text to the search box AND 566[SLEN]. Click "Go."
7) Click on the active link for the HA protein page.
Copy the accession number for the full-length HA protein. Click on the "BLAST Sequence" link (column on right side of page).
9) The BLAST page will pop up. The database should be set automatically to "non-redundant protein" and the algorithm should be "blastp." Click the BLAST button.
10) The BLAST report contains alignments of your search sequence against sequences in the database. The regions of the protein that is most likely to change show up as blank spaces.
11) Repeat Steps 1-10 with past flu seasons (2001-2008) and compare. Use the strain which the greatest number of flu strains related to it. It is found in the section called “Antigenic Characterization.”
-computer with Internet access
My hypothesis is that flu viruses from different seasons do not mutate in the same regions of protein because they are from different strains.
BLAST (Basic Local Alignment Search Tool) is the online tool used in this experiment. It can be found at:
www.ncbi.nlm.nih.gov/BLAST. BLAST is a set of programs used to find alignments between a nucleotide or protein sequence, and nucleotide or protein sequences within a database. I used protein blast because I had amino acid sequences. Protein BLAST is BLASTp. There is no sequence in the query box because I use accession numbers. Accession numbers are numbers given to a sequence so that the publishers can track the different versions of it. After you click BLAST, then there is a list of alignments. The crosses and spaces refer to changes. The reason why the crosses are not counted in the mutations is because these changes are conservative, meaning if they were changed, survival of the virus would be difficult.
From my results, my hypothesis was incorrect. There were two years where the protein had mutated in the same region. However, this was due to the same strain of influenza being prevalent in the two years. My explanation of why the regions of protein where mutations take place would be the same was correct, though.
Please answer the questions from October 2 to current.
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