Abstract

Objective

In this science fair project, you will use a special, free, Web-based computer tool called BLAST to analyze and estimate the effectiveness of different flu vaccines.

Introduction

Influenza is caused by a virus that attacks the upper respiratory tract (i.e., the nose, the throat and the lungs). Cold and dry weather allows the virus to survive longer outside the body than in warm weather. Therefore, in temperate regions like North America, when we are planning to enjoy Halloween, Thanksgiving or Christmas, it is also the time when we or our family members have a higher chance of getting the flu.

There are three types of influenza virus: A, B and C. Type A can infect humans, other mammals and birds and can spread fast and affect many people. Types B and C affect only humans and type C causes only a mild infection. Influenza type A viruses are sub-typed into two categories based on proteins (H and N) on the surface of the virus. The virus uses the H protein molecule to latch on to the host's cell and uses the N protein molecule to spread the infection. Types A and B continue to evolve genetically, with continuing changes to the amino acid sequence of the H and N proteins, and thus prevent the hosts from enjoying any prolonged protection against the virus. Aren't they smart?

The influenza vaccine typically contains three virus strains, two are subtypes of type A and one is of type B. The vaccine stimulates a protective immune response, particularly against viral surface antigens specific to the viral strains. Every February, the World Health Organization (WHO), based on the analysis of various laboratories across the globe, will decide what influenza virus strains to include in the vaccine for the new year.

The vaccine DNA sequence that encodes the viral surface proteins is a fragment of the DNA from each strain. If you imagine that you can hold the DNA fragment with both hands and stretch it out, you will then have a linear DNA sequence in your hands. The DNA sequence holds the genetic instructions for an organism. Unlike the English alphabet, which has twenty-six letters, the DNA alphabet has only four letters (A, C, T, G) and, while each English word is made of one to many letters, the genetic word (each of which specifies an amino acid) is always made up of three DNA letters.

It is easy to align two English words and compare their spellings. Even so, there is often more than one possible alignment:

For example, Alignment #1 (with red showing where the letters match)

or, Alignment#2 (shifting the word blueberry to the right by one character)

For the two words chosen above, alignment #2 gives us a better result than alignment #1. Similarly, you can take two genetic sequences and compare if their spelling is alike; this is called sequence alignment in bioinformatics. If they are very much alike, they may hold similar genetic instructions for the organism.

The alignment example above is simple enough that we can do it manually. However, when we want to align two DNA sequences, they can be over 1000 letters long and with only four letters, it is much more difficult and more time consuming to do it manually. Luckily, bioinformatics comes to the rescue. Bioinformatics is the collection and analysis of large amount of biological data using computers and computational/statistical methods.

BLAST stands for Basic Local Alignment Search Tool. It is a powerful Web-based tool for sequence alignment. It aligns your query sequence of interest to a collection of sequences stored in the computer and compares the results, telling you which sequences contain regions or segments that are similar to your sequence.

All else being equal, we would expect that a strong match between the DNA sequences encoding the surface antigens in the vaccine virus and the corresponding ones in the "wild" virus results in good protection against that virus. On the other hand, a poor match would result in weak protection against the virus. By using BLAST to measure the quality of the match, we can estimate the effectiveness of a vaccine against different viruses.

Terms, Concepts, and Questions to Start Background Research

To do an experiment in this area, you should do research that enables you to understand the following terms and concepts:

• Influenza (or flu)
• Flu notation
• Vaccine
• Virus
• Proteins
• DNA and DNA sequence
• Sequence alignment
• BLAST
• Genomics
• Bioinformatics

Bibliography

This article from the Centers for Disease Control and Prevention describes how strains of influenza are selected for vaccines.

• Centers for Disease Control and Prevention (CDC). (2009). Selecting the Viruses in the Influenza (Flu) Vaccine. Retrieved August 31, 2009, from http://www.cdc.gov/flu/professionals/vaccination/virusqa.htm

This site has BLAST, as well as a BLAST tutorial.

• National Center for Biotechnology Information. (2009). Retrieved August 31, 2009, from http://www.ncbi.nlm.nih.gov/

This site has sequence information as well as a BLAST tool.

• National Center for Biotechnology Information. (2009). Influenza Virus Resources. Retrieved August 31, 2009, from http://www.ncbi.nlm.nih.gov/genomes/FLU/growth.html.

This site shows flu activity by type and subtype. It includes historical information on past flu seasons. You can find information on the particular strains (either current or historical) in the "Antigenic Characterization" section of the CDC reports. You can use the strain information from the CDC reports to search the Influenza Sequence Database (above). For example, if the CDC report mentioned "Of the 65 influenza A (H3N2) viruses, 54 were characterized as A/California/07/2004-like...", the strain is "A/California/07/2004". If your database search turns up empty, make the search more general by removing the date information from the strain. In this example, the ISD entry is just slightly different: "A/California/7/2004". With patience and good searching strategy, you should be able to find the information you need.

• Centers for Disease Control and Prevention (CDC). (2009). Flu Activity & Surveillance. Retrieved September 2, 2009, from http://www.cdc.gov/flu/weekly/fluactivity.htm

• World Health Organization (WHO). (2009). Retrieved September 2, 2009, from http://www.who.int/en/

The National Institute for Allergy and Infectious Diseases (NIAID) launched this influenza virus database in 2004 to serve as a comprehensive, freely available global public database and analysis resource for the study of influenza viruses. This site has sequence information, as well as a BLAST tool.

• Influenza Research Database. (2009). Influenza Sequence Database and Bioinformatic Tools. Retrieved August 31, 2009, from http://www.biohealthbase.org/GSearch/home.do?decorator=Influenza

Experimental Procedure

First, study the above Terms and Concepts. It's especially important that you research and understand flu notation.

How to retrieve the protein sequence for hemagglutinin in strains of influenza used as vaccines, and BLAST it.

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. Open a new page that has information about past flu seasons. Click on "Go" next to the year of choice. For example, click on "Go: 2006–2007 Influenza Season Summary."
3. Read the information on the page.
• In particular, find the paragraph with the heading "COMPOSITION OF THE 2006–07 INFLUENZA VACCINE":
• It will tell you the name of the virus strains that were selected for use as vaccines. For example, "The Food and Drug Administration's Vaccines and Related Biological Products Advisory Committee has recommended that the 2006–07 trivalent influenza vaccine for the United States contain A/New Caledonia/20/99-like (H1N1), A/Wisconsin/67/2005-like (H3N2), and B/Malaysia/2506/2004-like viruses."
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 in the search box.
• For example, copy and paste "A/Wisconsin/67/2005" into the box near the text "search for."
• Full-length HA is 566 amino acids. In order to retrieve full length-entries, add this text to the search box AND 566[SLEN]. The search text in this example is "A/Wisconsin/67/2005 AND 566[SLEN]."
• Click "Go."
6. Click on the active link for the HA protein page. See this example.
7. Copy the accession number for the full-length HA protein.
8. 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."
10. Click the BLAST button.
11. The BLAST report contains alignments of your search sequence against sequences in the database.
• One type of information that you could gather from the BLAST output is the region or regions of the protein that are most likely to change. These regions show up as lowercase letters in the alignment.

Variations

Here are two potential experiments you can perform using sequence alignment techniques on influenza viruses. Pick a past year for which you have data on the DNA sequences in the flu vaccine as well as information about the prevalent flu outbreaks. Better yet, pick several such years so you can compare one to another.

• Based on sequence alignment, was the vaccine effective?
• If you could travel back in time and re-design the flu vaccine for the year you pick, which flu virus strains would you use for the vaccine? Based on sequence alignment, if the choice of virus strains you suggest are not available, are there any alternative strains you can use and still have an effective vaccine?

• For more science project ideas in this area of science, see Genetics & Genomics Project Ideas.

Credits

Last edit date: 2011-10-26 14:56:09