Biology of SARS-Cov-2

INTRODUCTION: SARS-CoV-2 is a virus that, starting in 2020, has caused the largest global pandemic in recent history. The disease caused by this virus, COVID-19, has affected millions of people worldwide. In this activity, you’ll watch the animation series Biology of SARS-CoV-2 and answer related questions to check your understanding. The concepts you’ll learn will help you better understand COVID-19 and coronaviruses, as well as other viruses and outbreaks in the past, present, and future. PROCEDURE: There are three animations in this series. Watch each animation, pausing between animations to answer the questions below in the spaces provided. PART 1: Infection Watch the first animation, Infection, which shows how SARS-CoV-2 infects and replicates inside human cells. 1. Explain how the terms COVID-19, SARS-CoV-2, and coronavirus mean different things. SARS-CoV-2 is the virus that causes Covid-19 and a specific type of coronavirus, Covid-19 is a disease . Coronaviruses are a family of viruses. 2. The diagram to the right represents a SARS-CoV-2 virus. In the table below the diagram, identify each of the labeled structures. Write one or two sentences describing the role of each structure in the virus’s replication process. Label Structure Role in Replication 1. RNA genome The RNA genome carries the virus’s genetic information, it has the genes for proteins that the virus uses to make copies of itself. 2. Protein Spikes The spike proteins bind to specific proteins on the surface of a cell, allowing the virus to enter the cell. 3. Envelope membrane The envelope gives the virus its shape and protects the virus’s genome so that it can be replicated. As shown in the animation, SARS-CoV-2 binds, or attaches, to specific proteins on the surface of a cell. These proteins are called receptors. Scientists have determined that SARS-CoV-2 binds to the same type of receptors on human cells as a different coronavirus that caused an outbreak in 2002–2004 did. That outbreak caused fewer infections and deaths than the SARS-CoV-2 outbreak. 3. Scientists discovered that SARS-CoV-2 is 10 to 20 times more likely to bind to these receptors than the other coronavirus was. Predict how this increased chance of binding has affected SARS-CoV-2’s ability to replicate. Since SARS-CoV-2 is 10-20 times more likely to bind to the receptors, it is more likely to enter cells and produce copies of itself. This increases the chance of binding and improves SARS-CoV-2’s ability to replicate and spread throughout the body. 4. Each of the following statements describes a step in the replication of SARS-CoV-2. These steps are listed in random order. Read through the steps and, in the spaces provided below, list them in the order they occur in the human body: a. The virus releases its RNA genome into the cell. b. Viral RNA polymerase helps transcribe more copies of the virus’s RNA. c. The virus binds to a receptor on a human cell’s membrane. d. New viruses travel to the cell membrane of the infected cell and are released outside the cell. e. The virus’s RNA is translated into proteins by the cell’s ribosomes. Correct order: c, a, e, b, d 5. As shown in the animation, SARS-CoV-2 uses the ribosomes inside human cells to translate its RNA into viral proteins. According to the animation, what is one of the viral proteins made by the ribosomes, and how does that protein help SARS-CoV-2 make more copies of itself? One of the viral proteins made by the ribosomes is viral RNA polymerase, which is needed to replicate the virus’s genome. The polymerase makes copies of the virus’s RNA which are used to make new viral genomes and proteins that combine to make new viruses. PART 2: Evolution Watch the second animation, Evolution, which shows how SARS-CoV-2 and other viruses may change over time due to mutations. 6. The SARS-CoV-2 virus has an RNA genome made of 30,000 nucleotides. List the four different types of nucleotides found in the SARS-CoV-2 genome. Adenine, Uracil, Cytosine, and Guanine When SARS-CoV-2 replicates, mistakes can be made in some copies of its genome, giving rise to mutations. Mutations happen randomly and are a source of genetic variations, or differences, among viruses. 7. Could these mutations make the virus more deadly to humans? Support your answer in one or two sentences. Mutations can make the virus more deadly, if they help the virus replicate or infect cells more easily. A common way to prevent infectious viral diseases, such as COVID-19 and the flu, is to develop a vaccine for the virus that causes them. Vaccines can be made from a virus’s proteins or other parts, or from a virus that has been inactivated and is no longer harmful. Some vaccines, such as the flu vaccine, need to be modified every year to keep up with changes in the virus. Studies have shown that SARS-CoV-2 has a slower mutation rate than the influenza virus, which causes the flu. This means that mutations occur less frequently in SARS-CoV-2’s genome than in the influenza virus’s genome. 8. Based on the information above, explain why it may be possible to develop a SARS-CoV-2 vaccine that would not have to be modified as often as the flu vaccine. SARS-CoV-2 has a slower mutation rate than the virus that causes the flu. So that means that SARSCoV-2’s genome and the proteins it has won’t change as often as the flu virus. Vaccines mostly target specific viral proteins and don’t need to be changed if the proteins change in structure. Since SARS-CoV-2’s proteins aren’t changing as often as the flu virus, the SARS-CoV-2 vaccine probably won’t need to be modified as often as the flu vaccine. Scientists at Arizona State University sequenced SARS-CoV-2 genomes collected from hundreds of infected individuals. They found a deletion of 81 nucleotides in some of the viruses. This large deletion is in a gene that codes for a protein that helps the virus escape the immune system. 9. Predict how the frequency of viruses with this deletion will change in the population over time. Use evidence to support your answer. This deletion would most likely reduce the protein’s function and make it harder for the virus to escape the immune system. Viruses with this deletion would have a disadvantage since they are more likely to be destroyed by the immune system and would then be less/small in the population over time. 10. How could sequencing many SARS-CoV-2 genomes be used to track how the virus has changed over time due to mutations? You could compare the genome sequences of SARS-CoV-2 samples taken from people in different locations. If there are variations among the genomes you could track when and where these variations were present and determine when related mutations happened. PART 3: Detection Watch the third and final animation, Detection, which shows several ways to test whether someone has been infected by the SARS-CoV-2 virus. The animation discusses two types of tests used to determine whether someone has an active SARS-CoV-2 infection. The table below compares some aspects of these tests as of August 2020. 11. Imagine you are planning to visit a family member who is a nursing home resident. The nursing home requires that all visitors test negative for an active SARS-CoV-2 infection no more than two weeks before the visit. Which of the two tests shown above would you choose, or what other information would you want to learn before choosing? Use evidence from the table to support your answer. I would choose the RT-PCR test because it has fewer false negatives and it doesn’t have to be repeated. Since the nursing home wants to test two weeks before, the RT-PCR test would be a better option. The antigen test can be somewhat risker to take because it can be less accurate since it is so fast. 12. In addition to the tests described above, people can also get tested for the presence of SARS-CoV-2 antibodies. Explain how an individual could test negative for an active SARS-CoV-2 infection and positive for SARS-CoV-2 antibodies. The individual could test negative for an active infection and positive for antibodies if they were infected in the past and recovered. Since they recovered, they will no longer have the virus. However, they will still have antibodies from having the virus before.