annotated-Pre Lab Tracking Influenza Fall 2023-1

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University of Kansas *

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Biology

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Feb 20, 2024

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Pre-Lab Activity Influenza A H1N1 Fall 2023-1 1 Pre-Lab Tracking the Evolution of Influenza A H1N1 Virus Learning Objectives:  Explain how evolution can occur rapidly in viruses through mechanisms of antigenic drift and antigenic shift.  Explain how mutations or changes in nucleotide sequence of viruses means hosts may not recognize the virus.  Use online databases, such as GenBank to analyze and interpret nucleotide sequence data Question:  What type of mutation (antigenic drift or antigenic shift) was responsible for the 2009 Influenza H1N1 outbreak?  Why did the influenza vaccine available in 2009 not provide protection agains the influenza virus in the population? Summary:  In this lab you will analyze nucleotide sequences from Influenza A viruses, specifically the nucleotide sequence that codes for the HA protein. These sequences were obtained from patients during the 2009 H1N1 Influenza pandemic. We will look at sequences of influenza prior to 2009 as well as the nucleotide sequence of the virus in the influenza vaccine. Materials Needed for Lab  Computer with access to the internet

Pre-Lab Activity Influenza A H1N1 Fall 2023-1 2 Background Influenza , commonly called the flu, is a highly contagious disease caused by influenza viruses. The flu can cause mild to severe illness, and at times can lead to death. Flu viruses spread mainly by tiny droplets made when people with flu cough, sneeze or talk. These droplets can land in the mouths or noses of people who are nearby. Less often, a person might get the flu by touching a surface or object that has flu virus on it and then Influenza, commonly called the flu is a highly contagious disease that is caused by influenza viruses. The flu can cause symptoms of headache, sore-throat, body aches, and high temperature; these symptoms are usually mild in healthy individuals. The influenza virus is responsible for 250,000 to 500,000 deaths a year. However, there have been influenza pandemics where influenza has been responsible for millions of deaths; 1918 Spanish flu, 1957 Asian flu, the 1968 Hong Kong flu, and the 2009 H1N1 flu. A pandemic is a worldwide spread of a new disease; an influenza pandemic occurs when a new influenza virus emerges and spreads around the world, and most people do not have immunity. There are three types of influenza virus; Influenza A, Influenza B and Influenza C. Influenza A can infect humans and many different types of animals including swine and avian. Influenza B and Influenza C circulate among humans. Influenza A is the most significant and most studied of the three types of viruses. Type A Influenza viruses are named after surface proteins that are present on the outside of the capsid. Influenza viruses produce 11 different surface proteins that attach to molecules located on host cells, such as those found in the respiratory system. Two of those surface proteins; hemagglutinin (H) and neuraminidase (N) are used to name the virus. For example, H1N1 has H type 1 and N type 1 surface proteins present on the viruses’ surface. Influenza A subtypes H1N1, H1N2 and H3N2 mainly infect humans.

Pre-Lab Activity Influenza A H1N1 Fall 2023-1 3 Figure 1. Influenza A virus https://www.urmc.rochester.edu/news/story/2493/computer-simulation-captures-immune- response-to-flu.aspx Tracking Virus Spread When you see a doctor for flu-like symptoms, the doctor may collect a swab of mucous or blood sample to be sent to an outside lab for testing. Sometimes this information is added to a database (without your identifying details) to allow scientists to keep track of strains of viruses and bacteria present in populations. The Center for Disease Control in the United States hosts an application called FluView that contains information such as the number of documented cases, date and location of cases, and demographic information. The World Health Organization and other countries around the world also host databases that contain this information. When naming viruses to add to the database, scientists follow a standard nomenclature (Figure 2). This standard nomenclature allows for others to quickly identify the type of virus, the subtype, date collected and location collected. Figure 2. Standard nomenclature used to name viruses. Source: CDC.gov Overtime, the data collected builds a picture of how the virus is spreading. Epidemiologists and scientists use this information to monitor the progression of the influenza season as well as use this information to determine where to ship supplies of the influenza vaccine. This prevents surpluses of vaccines in some locations and shortages in other locations. Need for Yearly Influenza Vaccine A vaccine is often made with a weakened or killed form of the pathogen. By exposing the immune system to the weakened or killed form of the pathogen, it teaches the immune system to recognize and destroy the pathogen thus providing immunity. Many vaccinations provide immunity for a number of years; some even protect you for life. The composition of the influenza vaccine is reviewed and updated each year as influenza viruses evolve. Influenza viruses can develop or evolve within timeframes of months to years. Influenza viruses can evolve rapidly through antigenic shift allowing them to escape human immunity and a vaccine developed one year may not work the next.

Pre-Lab Activity Influenza A H1N1 Fall 2023-1 4 Evolution of Influenza Influenza is a virus that replicates quickly and is prone to replication errors or mutations in its RNA sequence. The influenza virus genome is a single strand of RNA. Over time, as the virus replicates, random changes to the nucleotide sequence occurs, creating many possible mutations. These mutations may be detrimental to the virus and even result in defective viruses, others will be neutral and some mutations may offer some type of advantage. In this way viruses transmitted from one person to another are related and may accumulate differences overtime. In the influenza virus genome, if mutations occur in the RNA segment that codes for the two surface proteins (H and N) on the virus, then your existing antibodies may not recognize the virus and will not bind to it. These small changes in the surface of the virus may accumulate overtime and result in the hosts’ immune system failing to recognize and respond to a virus. These small changes to the surface protein as a result of errors during RNA replication is called antigenic drift (Figure 3) Antigenic drift occurs in Influenza Type A and B viruses. Antigenic drift is ongoing and is the basis for evaluating the components of the infuenza vaccine each year. As these small changes accumulate, the effectiveness of the vaccine may decrease. Another type of mutation, antigenic shift (Figure 3) in influenza virus occurs when genes of a single strain, or genes of two different strains exchange genetic material. This may produce a novel combination of genes that has a survival advantage over other strains. Viruses that originate from different species (avian and swine) may take part in this process. Reassortment events, from human and avian influenza A viruses have been the source of pandemics. Antigenic shift happens less frequently than antigenic drift and only occurs in Influenza Type A viruses. When a new version of a virus emerges as a result of antigenic shift, it may cause major illness if it is not recognized by the hosts’ immune system. Additionally, the influenza vaccine that is available at the time, may not be effective and the manufacture of a second vaccine required. Figure 3. Illustration of antigenic shift and antigenic drift. Source: http://www.influenzacentre.org/aboutinfluenza.htm

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