Virology Introduction
Viruses have either a double stranded (DS) DNA, single stranded (SS) DNA, DS RNA, or SS RNA genome. SS RNA viruses can be (+) with a 5’ to 3’ RNA genome, or (-) with a 3’ to 5’ genome.
The following diagram outlines how RNA viruses replicate their nucleic acid and express their genes (make proteins). Coronaviruses are a Class IV virus.
- Give an example of each type of RNA virus according to the genome in the following diagram (Class III-VI). For example, you can give coronavirus for Class IV. (4 points)
Class III: Reovirus
Class IV: Coronavirus
Class V: Influenza virus
Class VI: Retrovirus
- What other viruses are Class IV viruses? Name at least two. (1 point)
Flaviviridae, Astroviridae
Coronaviruses
There were coronaviruses before SARS appeared on the scene in 2003! Refer to the following article:
3. Write a short paragraph about the history of coronaviruses from its discovery until 2021. (1 point) In 1965 a pathogen from a boy with a cold in the UK was cultivated and was notable as a virus that was unrelated to any other known virus at the time. The same happened again in 1966 and 1967, then in 68’ June Almeida first imaged coronavirus naming it so because of the virus’s fringe that are round and petal shaped similar to the solar corona of stars. In 2003 severe acute respiratory syndrome or SARS hit southern China, a newly discovered virus like one in 2004 isolated from a child with pneumonia and in 2005 from two patients with pneumonia. In 2012 yet another coronavirus was discovered and isolated from a man with kidney failure and pneumonia. Finally, in 2020 researchers discover SARS-CoV-2 or COVID-19 in Wuhan, China. The outbreak spreads worldwide killing estimated millions.
SARS-CoV-2 Genome and Structure
Go to the attached PDF entitled “A Structural View of SARS-CoV-2 RNA Replication Machinery” and refer to Section 2 and 3.1 and Figure 1.
- What could be an advantage of being a virus with a genome that acts like mRNA? (1 point)
When the virus takes over a cell it infects RNA acting as mRNA which is translated by ribosomes to produce viral replicate enzymes that create new viral genomes and then assemble new viral particles.
- The virus does not have ribosomes. How is the viral RNA going to be translated? (1 point)
This can be done with the host cells ribosomes.
- What features on the genome are similar to eukaryotic mRNA? (1 point)
Proofreading and capping occurs, it possesses a 5’-cap and 3’poly(A) tail.
7. The genome also contains 5’ and 3’ untranslated regions. What does that mean? (1 point) (This is not a trick question and should be straight forward. Look at the terminology.)The RNA can act as mRNA for immediate translation of viral polyproteins. The untranslated region helps regulate RNA replication and transcription.
8. The term polycistronic was introduced in genetics when comparing the gene expression of prokaryotes and eukaryotes. The SARS-CoV-2 genome is described as polycistronic. Define the term polycistronic. (1 point) Containing the genetic information of a number of cistrons.
9. What is an open reading frame? (1 point) ORFs encode replicase polyprotein 1a (PP1a) and polyprotein 1ab (PP1ab)
10. What is a nonstructural protein? (1 point) It is a protein encoded by a virus that is not part of the viral particle.
11. How many nonstructural proteins does SARS-CoV-2 make? (1 point) Nine
12. How does the polyprotein 1ab become separate proteins? (1 point) It is cleaved into smaller proteins which is important in the transcription process of the RNA.
13. What are some of the roles for the nonstructural proteins? (1 point) Blockage of innate immune responses in infected cells, RNA binding, RNA-directed RNA polymerase, molecular connectors that enhance efficiency of RNA replication, help form complex replicase machinery, RNA capping and proofreading, stopping host gene expression
14. When we recently discussed transduction in class, we talked about the ability of a bacteriophage stopping its host cell from gene expression. What SARS-CoV-2 nonstructural protein stops host gene expression? (1 point) Nsp1
15. What is a structural protein? How many structural proteins does SARS-CoV-2 have? (1 point) They are a category of proteins that are responsible for cell function, there are four in SARS-CoV-2
16. Refer to Figure 4 in the following article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194867/#:~:text=Coronaviruses%20(CoVs)%20 are%20a%20group,as%20they%20harbor%20the%20viruses.
Name the structural proteins and describe where they are located in the virus. (4 points) Spike, envelope, membrane, nucleocapsid also known as E, M, N and S proteins. Spike and envelope proteins are embedded in the membrane protein that encapsulates the virus while nucleocapsid proteins are found inside the virus.
17. Referring back to the PDF entitled “A Structural View of SARS-CoV-2 Replication Machinery” (Figure 1), we see 9 accessory factor coding regions at the 3’ end of the genome. Refer to https://virologyj.biomedcentral.com/articles/10.1186/s12985-020-01402-1, Background (Information), paragraph 5. What is the role of accessory factors or accessory proteins? In your answer, address how necessary they are for the virus. (1 point) They are integral to viral pathogenesis; they modulate signaling pathways and the production of cytokines.
SARS-CoV-2 Variants of Concern
Refer to: https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/scientific-brief-emerging-variants.html; scroll down to “Emerging Variants”
Three variants of concern are UK B.1.1.7, South Africa B.1.351, and Brazil P.1
18. What area of the genome has mutated for all three of these variants? Is this part of a nonstructural or a structural protein? (1 point) For B.1.1.7 has a mutation in the receptor binding domain, B.1.351 has mutations in the spike protein, P.1 has three mutations in the spike receptor binding domain, all three have mutations on the spike protein which is a structural protein.
19. Why is a mutation in the above area so important? (1 point) This mutation may neutralize current vaccination attempts. The vaccine currently targets the spike protein of the coronavirus producing a polyclonal response but these three mutations evade immunity induced by vaccines changing our entire approach to the curing of this virus.
The following information is not necessary for this assignment, but might be of interest to you.
SARS-COV-2 “life” cycle:
Citations:
Liu, D. X., Fung, T. S., Chong, K. K.-L., Shukla, A. & Hilgenfeld, R. Accessory proteins of SARS-CoV and other coronaviruses. Antiviral Research 109, 97–109 (2014).
Shaffer, D. C. The Baltimore Classification System. News (2019).
Sheth, R. The Role of Replicase Polyprotein 1ab in SARS-CoV-2 and the Analysis of its Cleavage Sites. Young Scientists Journal (2021).
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