1.  Give an example of each type of RNA virus according to the genome in the following diagram

Class III-Rotavirus

Class IV-Coronavirus

Class V-Rhabdovirus

Class VI-HIV

2.  What other viruses are Class IV viruses? Name at least two.  (1 point)

Astrovirus and Flavivirus

3.  Write a short paragraph about the history of coronaviruses from its discovery until 2021.  (1 point)

First discovered in the 1960’s coronaviruses take their name from the spiked protiens of it’s outer layer. In 1965 a coronavirus B814 was isolated. This was followed by 229E which was discovered at the University of Chicago. In 1967 virus OC43 was discovered. The following year in 1968 they were all linked under the family of coronaviruses. In 2003 SARS was isolated followed by HKU1 in 2005. Another coronavirus MERS-CoV was discovered in 2012 followed by SARS-CoV-2 in 2019. 

4.  What could be an advantage of being a virus with a genome that acts like mRNA?  (1 point)

Having a genome that acts like mRNA is an advantage because it can be translated upon entry into the host cell.

5.  The virus does not have ribosomes.  How is the viral RNA going to be translated? (1 point)

Once inside the cell, the infecting RNA acts as a messenger RNA (mRNA), which is then translated by host ribosomes to produce the viral replicative enzymes.

6.  What features on the genome are similar to eukaryotic mRNA? (1 point)

A 5′-cap and a 3′-poly(A) tail are features on the genome that are similar to eukaryotic mRNA.

7.  The genome also contains 5’ and 3’ untranslated regions.  What does that mean?  (1 point) 

The 5’ and 3’ untranslated regions refer to the areas on either side of the coding sequence on a strand of mRNA. These regions are not translated into protein. 

8.  The SARS-CoV-2 genome is described as polycistronic.  Define the term polycistronic. (1 point)

Polycistronic described when two or more separate proteins are encoded on a single molecule of mRNA.

9.What is an open reading frame?  (1 point)

An open reading frame is part of a reading frame or sequence of nucleotide triplets specifying an amino acid that does not have stop codons.

10.  What is a nonstructural protein?  (1 point)

A non-structural protein is a protein that is encoded by a virus but isn’t a part of the virus particle.

11. How many nonstructural proteins does SARS-CoV-2 make?  (1 point)

There are 16 non-structural proteins.

12.       How does the polyprotein 1ab become separate proteins? (1 point)

Polyprotein 1ab is cleaved at the C-terminus at 11 sites.

13.       What are some of the roles for the nonstructural proteins? (1 point)

Suppression of host gene expression and the blockage of innate immune responses in infected cells.

14. What SARS-CoV-2 nonstructural protein stops host gene expression? (1 point)

Nsp1 stops host gene expression.

15.  What is a structural protein?  How many structural proteins does SARS-CoV-2 have? (1 point)

A structural protein is a protein that control cell shape and movement. SARS-CoV-2 has four structural proteins.

16. Name the structural proteins and describe where they are located in the virus. (4 points)

The four structural proteins are spike an outer glycoprotein, envelope, membrane a transmembrane glycoprotein and nucleocapsid which is within the phospholipid bilayer, they are located at the 3’ end of the genome.

17. What is the role of accessory factors or accessory proteins?   

Accessory proteins a play a role in viral pathogenicity or spread by modulating the host interferon signaling pathways. 

SARS-CoV-2 Variants of Concern

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)

The area of the genome that has mutated for all three variants is a spiked protein. This is a structural protein.

19.       Why is a mutation in the above area so important?  (1 point)

The mutation to the spike protein is important because it changes the structure of the protein and the spike region is what current vaccines target.