Coronavirus Lab

Part 1
1.

In your own words, describe how scientists figured out the source of the new coronavirus.

Scientists discovered the source of the corona virus by creating a map of the genetic information
of the corona virus infecting human and then compared it to other types of corona virus to
create an evolutionary tree and from that they were able to determine that the virus was likely
infecting bats who passed it on to pangolins who passed it on to humans.

2.

In your own words, describe the evolutionary evidence that suggests that the new coronavirus
is now spreading directly from human to human.

Since the strands of corona virus infecting humans are more closely related to other strands that
infected human than the strands that infected other animas which would suggest that the virus
made only on jump from pangolin to human since we would see more variation in between
strands that infected humans had people been getting it from animals.

3.

What do coronaviruses use as genetic material?

The corona virus uses RNA as its genetic material.

4.

What factors seem to make coronaviruses particularly good at jumping species barriers to
infect human populations?

The two main factors making corona good at jumping between species is because it had already
infected mammals which made it easier to infect other mammals like humans and secondly
because it uses RNA which is more prone to errors or random mutations than DNA.

5.

In your own words, describe why having a high mutation rate allows a virus to quickly adapt to
a new host.
The high mutation rate helps the virus adapt to a new host because the large amount of genetic
variation means there is a larger chance of one of the strands being able to survive inside of the
host and reproducing with its more favorable traits that allows it to adapt quicker.

6.

Imagine that scientists are studying a new infectious disease. They study the genomes of virus
samples taken from different patients and build an evolutionary tree. The tree shows that the
samples from humans are all closely related to viruses from mice. They are more distantly
related to viruses found in possums. However, the human samples do not form a cluster, or
clade. Instead they are spread out over the tree, and some are most closely related to other
human viruses, but others are more closely related to mouse viruses than they are to other
human samples.

1.

Based on this evidence, what do you think the source of the new disease is? Explain your
reasoning.

From the evidence the disease likely started in possums since it is distantly related to the strand
found in humans and then spread from possums to mice and then the mice spread it to humans
since the human virus is most closely related to the mouse virus and then it is passed to humans
by both other humans and mice since the human samples don’t form a cluster showing that
humans are being infected by things other than just humans.

2.

Based on this evidence, how many times do you think the virus jumped to humans from
another species? Explain your reasoning.

This could show that the virus jumped from mice to humans multiple times since the strands are
very closely related and there is no cluster so the mice could be infecting the humans just as
frequently as other humans.

3.

Based on this evidence, do you think the virus is spreading from human to human? Explain
your reasoning.

Yes, the virus is spreading from human to human since some of the human strands are similar
but due to the fact that the mice strands are also very similar to other human strands it could
show that humans are also being infected by mice.
 Part 2
1. Who are the authors of this research paper?
Kristian G. Andersen
Andrew Rambaut 
W. Ian Lipkin 
Edward C. Holmes 
Robert F. Garry 

2. The article is titled:

The proximal origin of SARS-CoV-2 and the authors state in their introduction:
“Here we review what can be deduced about the origin of SARS-CoV-2 from comparative
analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2
genome and discuss scenarios by which they could have arisen.”
In your words, what are the authors saying their paper is about?

They say that the paper is a comparative analysis of SARS-CoV-2 genomic data and a
perspective on the important features of the SARS-CoV-2 genome and a discussion
of the scenarios in which the features may have appeared.

3. In the section “Notable features of the SARS-CoV-2 genome”, what human

receptor molecule do the researchers claim SARS-CoV-2 binds to?

They claim that the SARS-CoV-2 binds to the ACE2 human receptor molecule.

4. Post one reference that the researchers cite to support the above claim.

Wan, Y., Shang, J., Graham, R., Baric, R. S. & Li, F. J.
Virol. https://doi.org/10.1128/JVI.00127-20 (2020).

5. Why do researchers include citations like the above when referencing

information?

They include these cites in order to give credit to the source where they obtained
the information and to maintain credibility in the science community.

6. The researchers state that:

“The receptor-binding domain (RBD) in the spike protein is the most variable part of the
coronavirus genome”
a. What is a “genome”?

All of the genes and genetic material inside of a cell, organism or virus.

b. The genome of SARS-CoV-2 is made of RNA, when RNA is brought to a cell’s

ribosome, what is made as a result?

Proteins are created when the RNA is brought to the ribosome.

c. Identify a “spike protein” in the image of SARS-CoV-2 below.

The spike proteins are the yellow colored spikes extending from the center of the
virus.

d. Suggest what the job is of the “receptor binding domain (RBD)” referenced by
the
researchers.

The receptor binding domain is responsible for connecting the virus to the ACE2
receptors.

e. Describe what it means if part of a genome is “variable”. Use the following terms
in your description: (mutation, mutation rate, selection pressure, evolution)

A part of a genome is variable if its mutation rate or selection pressure changes as a

result of its environment because it is forced to evolve to survive in each
environment so it mutates at varying rates.

7. The researchers identify two unique features of the SARS-CoV-2 genome that
distinguishes it from other coronaviruses.

a. What are these two features? (hint: look at the notes on Figure 1 in the paper)

The two features are the mutations in the contact residues of the spike proteins and
the acquisition of poly basic cleavage site and O-linked glycans.

b. For which feature are the researchers unsure about the function?

They are unsure about the function of the poly basic cleavage site and O-linked
glycans.

c. What is the function of the other feature? (hint: look at question 6d)
The receptor binding domain is responsible for connecting the virus to the ACE2
receptors.