SARS-CoV-2

Which of the following is not encoded in the viral RNA?

Envelope of the viral particle (The viral envelop is formed from by the budding off from the endoplasmic reticulum and Golgi bodies of the host.)

Which SARS-CoV protein has homology to the palm, thumb, and fingers domains of DNA polymerase?

RNA dependent RNA polymerase (RdRP)

What is the main function of the protein spikes?

The spikes have affinity for the ACE2 protein found in the membrane of the host lung epithelial cells. The spikes allow the viral particle to initially attach to the host membrane and then promote the fusion of the viral envelope with the host cellular membrane.

True/False The R-Naught (RO) value is not intrinsic to the virus, it depends on environmental conditions and the behavior of a culture or society.

True

What is the origin of the membrane envelope of the viral particle?

endoplasmic reticulum and the Golgi bodies of the host cell

Which two proteins encoded by SAR-COV-2 are translated from the positive strand RNA and are involved in adding or modifying the CAP on viral RNAs?

nsp 13 and nsp 15

The RNA dependent RNA polymerase and viral helicase are encoded by which of the following nonstructural proteins (nsp's)?

nsp11 and nsp 12

How long does COVID-19 live on polypropylene plastic?

3 days

The _______ protein attaches to the host ACE2 receptor and then promotes fusion of the host membrane with the envelop of the viral particle.

S

True/False The RNA viruses like to attach to the ACE2 receptors in our cells, which are found in large amounts inside our lungs.

True

True/False The only known tissue where the SARS-CoV-2 virus can replicate is in lung epithelial cells.

True

True/False The three S protein subunits form prominent "spikes" on the surface of the virus. One of the subunits has affinity for the ACE2 receptor, which is embedded in the membrane of host cells. These crownlike spikes give coronaviruses their name.

True

Label the numbers in the image showing the binding of the SARS-CoV particle to a lung cell.

1 - spike portion of spike protein (S1) 2 - ACE2 receptor on the outer surface of the human cell 3 - stem portion of spike protein (S2) 4 - Human protease that cuts at two sites within the spike protein to release the head portion (S1) and activate unfolding of the stem

SARS-CoV Spike protein: Label the parts of the spike protein.

1 - stem region 2 - region that is released by cut 2 (this allows the stem to unfold) 3 - Fusion domain that embeds into the host cell membrane 4 - transmembrane domain that is embedded in viral envelop 5 - cut site 1 (releases the top portion of the spike (S1) 6 - cut site 2: (releases the red region that allows the stem to unfold) 7 - glycan sugar moieties that hide the spike from the immune system) 8 - receptor binding domain

What are two reasons that SARS-CoV uses subgenomic RNAs?

1-This enables each of the coding regions to be translated 2-RNA recombination resulting from the "Jump and Copy" mechanism of the RdRP facilitates error correction by RNA recombination.

The first viral protein that is expressed in the infected cell is actually a series of multiple proteins translated together as a polyprotein. The polyprotein is cleaved into functional proteins by a viral-encoded protease. Question: How many proteins are derived from the original polyprotein?

16

What is the median incubation period for COVID-19?

5-6 days (The estimates range from 2-14 days with a median (most common value) of 5-6 days)

Which viral protein serves a proofreading function that protects the large genome of SARS-CoV from excessive mutations? (This protein has two activities. Its other function is to add a 5'-Cap to newly synthesized viral RNAs.)

ExoN (nsp 13)

True/False The only known tissue where the SARS-CoV-2 virus can replicate is in lung epithelial cells

False (It can replicate in many tissues that express the ACE2 receptor including cells of the oral and nasal mucosa, nasopharynx, lung, stomach, small intestine, colon, skin, lymph nodes, thymus, bone marrow, spleen, liver, kidney, and brain.)

True or False: One commonality between COVID-19 and a flu virus is that both of them must enter the nucleus to take control of the cell.

False (The COVID-19 viral particle contains a 30,000 base RNA (positive strand) that has a 5'-methyl cap and a poly(A) tail. It can immediately be translated on eukaryotic ribosomes because it already is capped: unlike the influenza RNA, which must first go to the nucleus to be capped before it can be translated in the cytoplasm. It makes a long polyprotein that is then cleaved into small peptides with discrete functions.)

What is the most common symptom of COVID-19

Fever (Fever is found in 87.9% of cases. The second most common symptom is the dry cough at 67.7%)

How does COVID-19 actually kill you?

It causes a very robust immune response throughout the lungs that causes inflammation of the alveoli. This inhibits gas exchange and causes the alveoli to fill with fluid.

In order to get rid of the virus on your skin, why is soap important?

It dissolves the lipid membrane envelope of the virus

During replication of the virus, which structural protein encoded by the virus embeds itself into the host membranes of the ER and Golgi complex and causes a region to bleb out to form the envelop of the viral particle?

Membrane (M) and Spike (S) proteins

The _____ protein(s) binds the 40S ribosome of the host and cleaves the 5'-end of host mRNAs, which removes the CAP and results in their degradation. It does not cut the viral RNAs because the virus has methylated the CAP of its own RNAs to mark them as viral.

NSP-1

Which protein protects the viral RNA, keeping it stable inside the virus?

Nucleocapsid Protein (N) This is similar to retroviruses that also have a similar protein; the nuclear matrix protein.

What is the best evolutionary rational for having the nsp's translated first before the structural proteins?

The nsp's encode enzymatic activities that prepare the way for replication processes which is an early step in the cycle. It makes sense that these proteins are synthesized first, because they are needed prior to assembly of the viral particle.

True/False S, E, M, and N are four structural proteins that are encoded by the subgenomic RNAs of the COVID-19 virus.

True In the genome map below, the genes on the left are the result of translating the positive strand. Genes on the right (transcripts 1-7) are encoded by the subgenomic RNAs.

Which pair of nsp's form a primase to assist the RdRp?

nsp7 and nsp8 (nsp7 and nsp8 = form a hexadecamer (16 subunits) with primase activity. They synthesize longer than normal primers for the RdRp)