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The SARS-CoV-2 Virus

A Close-up of SARS-CoV-2

How does the Covid-19 virus take over cells?

Cell infected with SARS-COV-2 (yellow). Scanning EM Credit: NIAID

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What is a Living Thing?

Nucleus (DNA)

Mitochondria

Cytoplasm

Golgi

ER

Ribosomes

A living thing:

✔︎ Is Made of Cells

✔︎ Has DNA (genetic material)

✔︎ Maintains Homeostasis

✔︎ Reproduces

✔︎ Metabolizes Energy

✔︎ Responds to Stimuli

✔︎ Grows and Develops

Human cells

8-100 μM

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Viruses Are Nonliving Parasitic Particles

Human cells

8-100 μm

Viruses:

🚫 1. Not a cell (no organelle structures)

✔︎ 2. Has *RNA or DNA (Genetic material)

🚫 3. Can’t Maintain Homeostasis

🚫 4. Can’t Reproduce on its own

🚫 5. Can’t Metabolize nutrients

🚫 6. Can’t Respond to stimuli

🚫 7. Can’t Grow or Develop

~0.1 μm

~100 nm

SARS-CoV-2 is 100-1000x smaller than human cells

~size of a ribosome

Zoom-In

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Common Viral Structures

1. Nucleic acids DNA or RNA

2. Nucleocapsid = Capsid protein + nucleic acid

3. Accessory proteins

4. May have membrane envelope (most animal viruses)

Viruses have:

Human HIV	Bacteriophage	Influenza	SARS-CoV-2
dsRNA	dsDNA	-ssRNA	+ssRNA


(ds = double stranded, ss = single stranded, and +RNA can be directly translated into protein) Images: Creative Commons and BioRender.com

Capsid

Viral envelope

Capsid

Viral envelope

Capsid

Viral envelope

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Build a Virus Model of SARS Cov-2

Models describe or explain ideas or objects. Use Handout

SARS-CoV-2 genome is 30,000 bases long

~14 Viral Genes, ~29 potential proteins

Spike protein: binds to cells Blue plastic anchor

Ion channel: virus release

E-protein: assembly & release

M-protein: virus assembly

Envelope: encloses/protect virus Golf ball

RNA: genetic code Black wax

N-protein: protects RNA White wax

Inside view

SARS-CoV-2: shows spikes, “crown-like” Image Credit: NIAID-RML

Building the SARS-CoV-2 Model: Students need model materials, a student handout, and scissors (if available). Students build the virus model during the presentation. As you discuss each structure, students complete the top half of the student handout: adding the function of each structure and the corresponding color of the wax they choose for that structure.

Start by explaining that many animal viruses have a lipid membrane or viral envelope. In our model it is represented by the golf ball. Tell students: “Be on the lookout for hints about where the membrane comes from.” Ask students to predict what the origin of the membrane is. (Note: The holes in the golf ball do not represent holes in the virus.)
Students take the black wax string and wrap it around one of their fingers to create a mRNA helix. This represents the single stranded mRNA found inside the enveloped virus.
Next, take the white wax string and cut it into 6 small pieces. Create small white balls of “N-Protein” and attach it to the black wax RNA. This white string represents the N-protein or nucleoprotein. It’s role is to protect the mRNA from degradation.
Students insert the RNA and nucleoprotein complex into the golf ball lipid membrane envelope.
The blue plastic items in the kit represent the viral SPIKEs. Insert the small end of each spike into golf ball holes. The Spike is made of protein and is responsible for binding to the cell’s receptor. The spike is like a “plug”, which fits into a “receptacle” called ACE2.
Students choose one color of wax string to represent the M-protein; which is involved organizing viral assembly (in the ER-Golgi). Students take one wax strand and fold it in half, form a glob at one end, insert the other end into a golf ball hole. Press the glob so that it sticks to the ball. (repeat for all three strands of wax).
Students choose another color of wax string to represent the Ion Channel protein; which is involved in viral release. Student folds one wax string in half, forms a glob at one end, inserts the other end into a golf ball hole, then press the glob so that it sticks to the ball. (repeat for all three strands of that color)
Students use the last color of wax string to represent the E-protein, which is involved in both assembly and release of the virus. Separate all the wax strings and repeat as in step 6 and 7.
Students observe how simple or primitive the virion is as compared to a eukaryotic cell.
Viral genome is 30,000 bases long with ~14 Viral Genes and 29 Potential Proteins, the human genome is 3 billion base pairs long with 28,000 genes.

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5. Virus RNA replicase makes RNA copies

4. mRNA binds to ribosomes, which build virus proteins

How do our lungs become infected?

1. A person inhales the virus

2. Virus spikes bind ACE2, enters cell

7. The cell releases new viruses.

Lung Cell Nucleus

Lung Airway

6. New viruses assemble in ER-Golgi

3. Virus releases the RNA

How does a Cell become Infected with the virus?

1. The viral particle enters the lungs (most likely route of entry).

2. **The viral particle enters the cell via endocytosis when the viral Spike protein binds to the ACE2 receptor. ACE protein is found on lungs, arteries, heart, kidney, and intestines and other structures.

3. The viral particle releases the viral +ssRNA into the cytoplasm of host.

4. The viral RNA is +, i.e. it is the coding strand (sense strand) and therefore, the cell’s ribosomes immediately begin translating viral proteins. The amino acids and energy required is donated by the cell.

5. One of the viral proteins that are made, called “RNA Replicase”, is an enzyme that makes new copies of the viral RNA genome (30,000 bases long, 14 genes, codes for ~24 proteins). The RNA Replicase enzyme is not found in humans.

6. Once all the components of the virus are created, the virus will self-assemble into a new viral particle in the golgi apparatus. The viral membrane envelope is derived from the cell’s golgi membrane. Every time a person sheds virus, they are shedding proteins and lipids created in their own body.

7. The cell will release new virus particles via exocytosis or if the cell is overwhelmed, it may break open—by cell lysis—and release remaining virus particles.

**SARS-CoV-2 bind the ACE2 Receptor.

In order for a cell to become infected by SARS-CoV-2, it must have the ACE2 receptor. The spike protein on the virus’s surface, binds to ACE2 receptor on the cell and then is taken up by the cell via endocytosis. ACE2 protein is found on lungs, arteries, heart, kidney, intestines and other structures. ACE1 and ACE2 are similar proteins with similar functions, but the virus only binds to ACE2. The spike is like a “plug”, which fits into a “receptacle” called ACE2.

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SARS-CoV-2 Genome(link)

The RNA Genome is 30,000 bases, ~14 viral genes

Gene 8 mutations caused the jump from bat to human.

How do scientists share this information? (See link)

5’

3’

1a RNA Replicase

2 Spike

3a

E

M

6

7b

8

9a

10

1b RNA Replicase

3b

7a

9b

*

Spike protein

Ion channel

E-protein

M-protein

N-protein

RNA

SARS-CoV-2 “Genome”

This diagram shows a viral particle labeled with the key structures and the virus’s genome. The genome is composed of single stranded RNA (positive coding or “sense” strand is ready for translation) and it is approximately 30,000 bases long.

The boxes in the genome represent individual genes that correspond to the proteins in the diagram (RNA replicase is made inside the host, but not packaged into the virion). More than half of the genome codes for the RNA Replicase enzyme (1a and 1b are the codes for the subunits of replicase). There ~14 genes and ~29 proteins (translational differences give rise to proteins than genes, splicing does not occur). Some proteins have unknown functions at this time.

How do scientists share virus genetic information?

Visit the UCSC genome browser website to see the bioinformatics for Covid19 virus. Click on the “Bases” box to see the genetic code.

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Testing for an RNA Virus

1. Collect patient’s cells from nose or throat.

2. Extract the RNA from the sample.

3. Use reverse transcriptase enzyme (buy it) to convert all RNA to cDNA.

4. Use polymerase chain reaction to make MANY copies of one viral gene.

5. Use fluorescent technology to detect the presence of a Covid virus gene.

2

Extract RNA

Reverse transcribe

RNA into DNA

3

Patient’s cells

1

If viral gene is present, fluorescence is detected.

5

If viral gene is absent,

no fluorescence.

5

qPCR makes many copies of the viral “N” gene.

4

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Studying Small Segments of a Genome

… is like finding a needle in a haystack.

PCR makes trillions of copies of target DNA, greatly outnumbering other genes.

PCR

PCR uses DNA primers as “genetic bookmarks” (video link)

ATGA

CGCC

primer

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SARS-CoV2 Evolution

Learn more at Nextstrain.org/ncov

Bioinformatics compares virus seq globally
Creates a phylogenetic tree showing evolution
Branch points are a mutation in RNA seq
Branch length shows length of time
Colors show countries (USA red)

SARS-CoV2 Phylogenetic Tree 2020

December-2019

February

January

March

April-2020

Mutation Hotspots (as of 4-2020)

Diversity

5’

3’

1a RNA Replicase

2 Spike

3a

E

M

6

7b

8

9a

10

1b RNA Replicase

3b

7a

9b

SARS-CoV-2 is Mutating (Evolving)

NextStrain.org collects sequence data from around the globe for flu, ebola, Sars-CoV-2 and other infections diseases.

We can visualize how the virus has changed over time by sequencing their genome and creating a phylogenetic tree, which shows the relationship between the virus samples tested.
The x axis represents the date time. The dots reflect the date a virus sample was sequenced.
Dots sitting on the same line indicate identical genomes and branch points are created when the RNA sequence changes or mutates.
Each node reflects a change in genetic sequence.
The dates of nodes are inferred based on when their descendants were sampled and the rate at which the virus mutates.
Colors represent virus RNA sequences from different continents or regions of the globe. (Red is US and parts of Mexico. Green is European countries, Purple is Asian countries….

The lower diagram shows the virus’s genome and the graph above it shows the level of genetic diversity of nucleotides at that position. Large spikes are areas of the genome that are rapidly mutating.

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References

Callaway, E. The coronavirus is mutating—does it matter? Nature 585, 174-177 (2020) https://doi.org/10.1038/d41586-020-02544-6
Centers for Disease Control and Prevention: U.S. Covid-19 Vaccine Product Information. Visited 1-18-21. https://www.cdc.gov/vaccines/covid-19/info-by-product/index.html
Connors, M et al. SARS-CoV-2 vaccines: Much accomplished, much to learn. Annals of Internal Medicine 2021. https://www.acpjournals.org/doi/10.7326/M21-0111
Milken Institute: Covid-19 Vaccine and Treatment Tracker. Visited 1-12-21. https://covid-19tracker.milkeninstitute.org
NextStrain.org: Genomic epidemiology of novel coronavirus - Global subsampling, 01-18-21. https://nextstrain.org/ncov/global
Trougakos, I.P., Stamatelopoulos, K., Terpos, E. et al. Insights to SARS-CoV-2 life cycle, pathophysiology, and rationalized treatments that target COVID-19 clinical complications. J Biomed Sci 28, 9 (2021). https://doi.org/10.1186/s12929-020-00703-5
UCSC Genome Browser: SARS-CoV-2 Sequence, Jan. 2020/NC_045512.2 Assembly (wuhCor1). Visited 01-18-21. https://rb.gy/jsowwd
Zhou, P., Yang, XL., Wang, XG. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020). https://doi.org/10.1038/s41586-020-2012-7

(Some graphics were built using BioRender.com online software)