Biology - Chapter 1 Viruses

Monkeypox has DNA as its genome. Once the supplies of vaccine are more readily available, would you expect that once immunized, people would have to get repeated boosters like for SARS CoV 2? Why or why not?

Unlike CoV 2, whose genome consists of viral RNA, Monkeypox has DNA. Therefore, it's polymerase that replicates genomes has the ability to proofread its copies before going through with the replication. So, no mutations will occur unlike viruses with RNA polymerase which can't proofread during replication.

Some viruses have an envelope. How is a virus envelope analogous to in an eukaryotic cell?

Virus envelope is analogous to a eukaryotic cell's cell membrane.

What characteristics of living organisms do viruses also have?

Viruses are made of proteins and glycoproteins like cells do. They have a genome but it isn't always DNA. They evolve

How do viruses differ from cells in types of genomes?

Viruses can have RNA or DNA as their genome - the RNA or DNA genome can be single stranded, double stranded (actually genome is part of how we characterize viruses)

Which viruses are more likely to cause pandemics - Viruses with RNA genome or viruses with DNA genome? Why?

Viruses with an RNA genome b/c viruses with RNA don't have the ability to proofread, it often results in genome mutations or errors. Sometimes mutations allow the virus to have selective advantage making it easier to spread and infect more people. Also, mutations delay the cure/treatment development

1. How could sequencing many SARS-CoV-2 genomes be used to track how the virus has changed over time due to mutations?

You can see how many changes occurs and where plus more mutations = longer time that virus has been in population so can trace where virus started and where spread

Zoonotic

a virus that transmits from animals to humans

Vector

intermediate organism, to be transmitted from one type of host to another (ex. mosquitos)

Which pandemic(s) was not actually a pandemic: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(a) Swine Flu 1976

Which pandemic(s) is most closely related to chimps/non human primates virus.: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(b) HIV

Which pandemic(s) is transmitted by unprotected sex: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(b) HIV (g) Ebola West Africa 2014-6

Which pandemic(s) is caused by a virus that has the most errors in the genomes and is the most genetically diverse: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome)

Which pandemic(s) had an RNA genome: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(c) West Nile Virus

Which pandemic(s) spread by mosquitoes: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(c) West Nile Virus (h) Zika 2014-5

Which pandemic(s) linked to large hog farms in Mexico and import of swine from other countries: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(d) 2009 panH1N1

Which pandemic(s) is spread by aerosols: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(d) 2009 panH1N1 (f) SARS CoV 1 2003 (i) MERS (Middle Eastern Respiratory Syndrome)

Which pandemic(s) is linked to bats (either direct contact with bats or bat products or via other animal host): (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa (j) Ebola DRC 2018

Which pandemic(s) caused humans to be infected via contact with camels: (a) Swine Flu 1976 (b) HIV (c) West Nile Virus (d) 2009 panH1N1 (e) Nipah (f) SARS CoV 1 2003 (g) Ebola West Africa 2014-6 (h) Zika 2014-5 (i) MERS (Middle Eastern Respiratory Syndrome) (j) Ebola DRC 2018

(i) MERS (Middle Eastern Respiratory Syndrome)

Define virus

-an infectious agent that can only replicate/reproduce within a host organism -made of proteins (capsid) and genome (RNA or DNA) and some have an envelope (phospholipid membrane outside capsid)

All cells have __________ as their genome, but viruses can have _____________ and _____________ as their genomes.

1) DNA 2) DNA 3) RNA

What are four characteristics of viral genomes that may vary among viruses?

1) RNA or DNA 2) Single stranded or double stranded 3) One piece or many pieces 4) Linear or circular

SARS CoV 2 - What are two reasons that SARS CoV 2 is still spreading in US and world? Briefly defend your two reasons.

1) as the virus spreads, genetic mutations accumulate over time. Mutations increase the virus' ability to spread and adapt to its environment. In other words, some characteristics of viruses are changing all the time, and this makes it impossible for any country to catch up. 2) some regions, such as Africa, are too economically disadvantaged and have such poor medical infrastructure to have access to vaccines, or abilities to store, administer vaccines. At the same time, the huge population in some countries also leads to many patients who cannot be treated in time due to the insufficient number of medical staff, and the infection cannot be controlled in time. 3) I would add here that travel contributed to spread - as symptoms were minor, people traveled and spread virus 4) For US - Lack of strong national consistent public health message and strong emergency response - lack of masks, preventive measure for healthcare professionals , low % of vaccination allowed virus to continue to spread and mutate.

List 3 characteristics of all living organisms (there are a lot more than 3 so if you want to list more than 3 to better study - go for it)

1. Cellular organization (have cells) 2. They can reproduce 3. They grow and develop 4. Homeostasis 5. Ability to adapt

List four ways in which viruses can differ from each other.

1.) Size 2) shape of capsid (icosahedral or helical) 3) type of nucleic acid - RNA or DNA including double stranded or single stranded 4) envelope or not

As we discussed in class, influenza can undergo genetic shifts which often causes major pandemics. What is unique about influenza viruses that allows them to undergo genetic shifts?

A flu virus has 8 different pieces of its genome. Plus there are also swine flu and bird flu that also has 8 different pieces of its genome. Sometimes a cell (could be human but usually starts in swine or bird) is infected with 2 different flus (swine and human or human and bird) - they mix in cell so get new viruses that are part human/part bird or part swine/human — DANGER - new pandemic....that is what happened with 2009 H1N1 pandemic

In our cells, our genome which contains genes (information for making proteins) is in its own compartment, the nucleus, but ribosomes (that synthesize proteins) are in the cytoplasm. How does the information from the genome get to the ribosomes? Maybe a better way to ask this is: If DNA doesn't ever leave the nucleus, how is the information carried from the DNA to the ribosome?

A mRNA (messenger RNA) carries the information from DNA in nucleus to ribosomes in cytoplasm to make proteins.

There is a new viral outbreak on WFU campus. It is caused by the Demon Deac virus - anyone infected turns into the Demon Deacon after 3 weeks post infection. A) What mode of transmission would lead to a high infection rate on campus? B) Tests have been developed to detect individuals that are infected - What would be the most sensitive test - PCR (genome), antigen (had been exposed), or antibody (been vaccinated or had infection)? C) If this virus infection were to become a pandemic, is the virus genome more likely DNA or RNA? Why?

A) Aerosol transmission B) PCR - testing for genome is MOST sensitive test and detects lowest amount of virus component C) RNA, more strains due to there being mutations, which will require more vaccines, and thus will result in it being harder to combat. This is the case because mutations with a selective advantage will make the virus more infective and those strains will spread across the viral population

A monoclonal Ab recognizes and binds to one particular part of the spike protein and keeps it from attaching to cells A) Why would this work as an effective anti-viral? B) If Monoclonal Ab 1 worked really well against the delta strain of SARS CoV 2, why would it not work on the Omicron strain or other strains currently circulating in the population?

A) This ensures that the spike protein can't bind to the cell so then it no longer has hosts to keep replicating and spreading to. B) Since the virus mutated the monoclonal Ab might not recognize and bind to the part of the spike protein that is necessary in order for it not to be able to bind to the cell-not as effective in stopping binding of Spike to cells because so many mutations in Spike

The SARS-CoV-2 virus has an RNA genome made of 30,000 nucleotides. List the four different types of nucleotides found in the SARS-CoV-2 genome.

A, G, C, U (U is in RNA instead of T)

What is the difference between attenuated, replication capable virus vaccine and an inactivated or killed virus vaccine? A) In terms of viral component of the vaccine? B) In terms of adaptive immune response?

A. (1)Attenuated: Live virus is administered directly to the patient, able to replicate // It could have RNA or DNA genome - just the problem is that if RNA more likely to mutate and cause disease (2) Inactivated: DEAD/Killed, unable to replicate virus is administered to the patient, cannot mutate // could have DNA or RNA genome B. (1) Attenuated: both B cells and Tcells released - B cells release AB which will block virus from binding/entering cell; T cells, specifically cytotoxic T cells will attack and kill virus infected cells (2) Inactivated: only B cells released (see above)

What is the genome of all cells - bacterial or ours?

All cells have a genome that is double stranded DNA - no exceptions

Once the SARS CoV 2 vaccine was available, predict the outcome of the pandemic if 80-90% of population was vaccinated within the first month of vaccine availability

Although the virus will continue to mutate in response to the vaccine, in the grand scheme of things the outbreak will be greatly reduced and fewer people will be infected.

Reservoir

Animal host of a zoonotic disease (ex. bats, rodents, cows, pigs, sheep, swine)

How do antigen proteins trigger an immune response

B cells - Ab

How does an inactive whole virus trigger an immune response

B cells - Ab

Which of the following would more likely cause a pandemic that lasts years? Briefly, why? A) One that has 50% lethality and spread by bodily fluids B) One that has 2% lethality and spread by aerosols C) One that has 35% lethality and spread by ingestion

B) One that has 2% lethality and spread by aerosols

Why is HIV so genetically diverse?

B/c its RNA genome copies into DNA which is the most error prone process. It likely also had time to become genetically diverse due to the stigma surrounding the virus. As well as the HIV virus was circulating in African populations before spreading to Europe and America.

Each of the following statements describes a step in the replication of the SARS CoV 2. List them in the correct order that they occur in the human body. A) The virus releases its RNA genome into the cell B) Viral RNA polymerase helps copy the genome C) The Spike protein binds to a receptor on human lung cell D) The envelope of the virus and the plasma membrane of the cell fuse. E) New viruses travel to the cell membrane of the infected cell and are released outside of the cell F) The virus RNA genome is used by cell's ribosomes to synthesize the viral proteins G) RNA genomes and viral proteins self-assemble into new viruses

C, D, A, F, B, G, E

Explain how the terms COVID-19, SARS-CoV-2, and coronavirus mean different things.

Coronavirus is a group of viruses similar but not identical to SARS CoV 2 which causes COVID (disease)

3.

Envelope

The envelope is an outer layer that some, but not all, viruses have. How does an envelope form? What is an envelope analogous to in a eukaryotic cell?

Envelope is analogous to plasma membrane and it forms from plasma membranes of cells

Once the mRNA has entered a person's cells, it is integrated into the cells' DNA (T/F)

F

T or F. The genome of SARS CoV 2 is copied by the cell's polymerase

False - our polymerase can only use DNA as template to make more DNA - No cell has an RNA polymerase so if virus needs an RNA polymerase it has to make it in the cell (using cell ribosomes)

What is one reason that polio virus has been detected in New York, London and Israel?

Fewer people are getting vaccinated, and children born during COVID-19 or through home births will not necessarily receive their vaccines. Additionally, the Salk vaccine only offers B cell protection because it is an inactive virus which would provide less immune protection for the circulating vaccine strain of polio.

Scientists at Arizona State University sequenced SARS-CoV-2 genomes collected from hundreds of infected individuals. They found a deletion of 81 base pairs in some of the viruses. This large deletion is in a gene that codes for a protein that helps the virus escape the immune system. Predict how the frequency of viruses with this deletion will change in the population over time. Use evidence to support your answer.

Gene makes protein that helps virus escape immune detection. If that 81 bp deleted then virus more likely to be recognized by immune system so virus wouldn't reproduce as readily...therefore would decrease in % in population

How is a virus envelope like a cell membrane (plasma membrane)?

In a eukaryotic cell, the plasma membrane acts as the boundary made of phospholipids and proteins. These proteins act as pores to help move things in and out of a cell. Similar to a plasma membrane, the envelope acts as an outer wrapping of a virus. An envelope is formed when a part of the host cell membrane envelops the virus, forming an outer layer. Envelope is made of phospholipids and proteins just like cell plasma membrane

SARS CoV 2 - What is the most likely origin of this virus? Based on data we discussed in class, was it a lab leak or zoonoses? Briefly, why?

It was a zoonose, because there is no evidence for the lab leak but for the wild animal market. There was evidence that wild animals at the seafood market were carrying the virus according to our discussion in class.

What contributed to the 2009 H1N1 pandemic?

Large hog farms led to lots of opportunities for transmission. Trade, roots, and importation of hogs from multiple countries

What characteristics of living organisms do viruses share with our cells?

Made in cells (but not necessarily made up of cells) -evolution (especially RNA viruses) adaptation -genetic material and the ability to reproduce (but only if in a cell)

Why might people need another SARS-CoV-2 vaccination if the SARS-CoV-2 virus mutates?

Mutations in Spike might make Ab produced by earlier vaccine not as effective at preventing Spike from entering cells

When physicians and nurses returned to the US after volunteering with Doctors without Borders during 2014-16 Ebola Outbreak, people in the US were fearful of being in the same room and breathing the same air with asymptomatic physicians and nurses. Based on what you learned about Ebola, was that a likely way for Ebola virus to spread?

No, Ebola spreads through bodily fluids. Though the asymptomatic people could have been carrying the virus (extremely unlikely), they should not be worried about breathing the same air. It does not spread through aerosols.

What is one reason that monkeypox has become more widespread in recent years?

People stopped getting vaccinated against smallpox in the 80's, which is thought to be contributing to the recent rise in monkeypox cases. The smallpox vaccine is 85% effective against monkeypox, so individuals who have been vaccinated against smallpox would likely also be protected against monkeypox. Additionally, recent cases of monkeypox have presented as genital pain instead of a rash, so it may be harder to recognize.

From the virus's perspective, why is the host important?

REQUIRED for protein translation/protein synthesis - Virus needs cell's machinery to replicate

1.

RNA genome

What do all viruses require from a living cell?

Ribosomes - all viruses require cell ribosomes to make their proteins - big part of reason why they need a cell to replicate/reproduce

2.

Spike protein

Once the mRNA has entered a person's cells, it helps trigger the production of B cells (T/F)

T

Once the mRNA has entered a person's cells, it is eventually eliminated from the body (T/F)

T

Once the mRNA has entered a person's cells, it is translated into spike proteins (T/F)

T

You have been hired by CDC to advise them on future pandemic preparedness. Based on SARS CoV 2 pandemic response and monkeypox response in US, what would be your # 1 best advice to be better prepared for future pandemics?

Take the virus seriously before it spreads and becomes a pandemic (contact tracing, surveillance, etc... when one case arises), immediately optimize vaccine responses and development, distribute vaccines early on so that all countries are prepared, invest in healthcare in economically deprived countries, invest into education of diseases and viruses and encourage good hygiene practices, before pandemics begin, assess risks and gaps in healthcare

A friend of yours has refused to get the flu vaccine because it isn't natural - It is not like your own adaptive immune response. What would you tell them to explain to them how vaccines are natural?

The flu vaccine is an inactivated whole virus that injects virus into your body, so that when exposed to your immune system, you will naturally create antibodies. It mimics what happens in an infection without making you sick - it mimics a primary adaptive response so your body has memory cells — then when it is flu season and you get exposed to flu virus - memory kicks in fast and swift and no actually flu infection/disease - which is a secondary adaptive response. Body's B cells make antibodies that bind to virus to virus can't enter cells - virus key is blocked by antibodies so can fit in cell's lock

How does SARS CoV 2 "know" that it has found the cell that will allow reproduction of the virus?

The protein spikes (also called crowns) on the virus scan for the right cell to latch onto. Once they find the human cells, they latch and the plasma membrane of cell fuses with envelope (like a mini plasma membrane) so viral RNA genome gets in and hijacks the cell.

Why is a vaccine the most effective prevention for a viral infection?

The vaccine mimics the primary exposure to pathogens, so B cells or T cells are made specific to the pathogens proteins. When encountering the actual pathogen the memory cells will respond much faster and have a higher response

Once the RNA genome of SARS CoV2 gets into our cells, what happens next?

The virus can "take over" cellular ribosomes to make spike proteins and RNA polymerase. The RNA polymerase transcribes the RNA genome.These proteins and RNA genome self assemble into a full virus which is then able to leave the cell and infect other hosts. The virus may also prevent the cellular ribosomes from making its own proteins

Why are antibodies effective against SARS CoV 2 infection?

They attach to the spike on Sars Cov 2. Since the spike protein is what attaches to human cells it allows the virus to enter our cells. When this entrance is blocked, the infection is prevented.

Why would an unvaccinated person probably need more time to recover from a SARS-CoV-2 infection than a vaccinated person would?

They don't have memory B and or memory T cells that respond quicker and clear virus either before it causes disease or only minor disease

How does mRNA (genetic instructions) trigger an immune response

This mimics that virus is replicating in cells so trigger B and T cell response