BIOL 512 Exam 2 Study Guide Part 2

What are the different types of Influenza? Which ones infect humans?

Influenza A-D, Influenza B infects humans

What type of cell does Influenza infect?

Ciliated epithelial cells

What is the purpose of the muco-ciliary clearance system?

Protects the airways by trapping and removing inhaled pathogenic viruses, bacteria, nontoxic, and toxic materials.

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Consists of periciliary fluid, mucus, and cilia

Who is at most risk for Influenza infection? Do people die from direct flu infection or secondary bacterial infection?

Young children (

What is the receptor for influenza?

HA binds sialic acid residues on surface glycoproteins.

What is sialic acid? How does the type of sialic acid indicate host range? What are typical sialic acid linkages and where are these linkages observed?

Sialic acid is a terminal moiety on oligosaccharides.

Typically α(2→3)

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Birds= α(2→3)

Humans= α(2→6)

Pigs= α(2→3) and α(2→6)

Why are pigs considered a “mixing vessel” for new flu strains?

Pigs can be infected by both human and avian flu strains

What are the 3 components of Influenza polymerase? Which one is targeted by Xofluza?

PA: endonucleolytic cleavage, Xofluza target

PB1: 5’ + 3’ RNA binding polymerase activity

PB2: binding of the 7mG cap on the mRNA

What is cap-snatching?

Flu virus lacks capping machinery. Viral polymerase associates with actively transcribing RNA polymerase and cleaves nascent RNA to create cap.

What is thought to cause the switch from transcription to replication for Influenza?

The exact cause is not well-understood. It is currently thought to be dependent on NP levels. The more NP, the more likely cRNA synthesis is to occur.

What are the ways that Influenza encodes for multiple proteins from single transcripts?

There are only 8 genome segments, but 14 proteins are encoded. Two proteins are generated by splicing (M2 and NEP), 2 others are generated by leaky scanning, and another results from ribosomal frameshifting.

Why is Influenza unique in its use of RNA splicing? What proteins are created from alternative splicing?

Most viruses do not undergo splicing

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Two proteins are generated by splicing, M2 and NEP

What is the role of NA in the release of viral particles?

Congregation of membrane proteins M2, HA, and NA causes budding and scission.

What species contributed to the H1N1 pandemic in 2009?

2009 H1N1 contains gene segments from avian, swine, and human viruses.

What order are the CoVs in? What is the ancestral host for all CoVs? What are the different genuses of CoVs?

CoVs are in the nidovirus order.

Bats are the natural and ancestral host for CoVs

Genuses: alpha, beta, gamma, delta

What are some prominent CoVs of pigs? When and where did SADS-CoV emerge?

Porcine respiratory and reproduction syndrome virus (PRRSV)

Porcine hemagglutinating encephalomyelitis virus (PHEV)

Transmissible Gastroenteritis virus (TGEV)

Swine Deltacoronoavirus

Porcine Epidemic Diarrhea Virus (PEDV)

Severe acute diarrhea syndrome coronavirus (SADS-CoV)

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SADS-CoV emerged in 2017 in Guangdong province in China.

Which of the 4 cold-causing CoVs is associated with Croup? What are the 3 CoVs that have caused worldwide epidemics?

NL63 is associated with Croup

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SARS-CoV, MERS-CoV, and SARS-CoV-2 have caused worldwide epidemics.

What were the intermediate hosts of SARS-CoV? Where did a super spreader event occur for SARS-CoV and how was the virus contained?

SARS originated in bats, Chinese bats, Himalayan Palm Civets, and Racoon dogs were intermediate hosts.

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The super-spreader event occurred at Hotel M in Hong Kong.

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Virus was contained through quarantine measures.

What region of the world is MERS-CoV confined to?

MERS-CoV is confined to the Middle East.

What is the intermediate host for MERS-CoV? How far back have samples from this host been found that have are positive for MERS-CoV?

MERS-CoV likely originated from bats in Africa and camels are intermediate hosts.

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Positive MERS-CoV tests as far back as 1982

Why are the overall number of MERS-CoV infected humans relatively low?

The virus does not spread well in humans, people working closely with camels were more susceptible. African people did not get the disease.

Where did the SARS-CoV-2 outbreak begin?

In Wuhan, China, at the Huanan Wholesale Seafood market.

What data demonstrates that the virus likely emerged zoonotically in the HSM?

The genomic diversity before Feb. 2020 was composed of only 2 viral lineages, likely the result of two separate cross-species transmission events into humans.

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Environmental samples were spatially associated with live mammals that were previously known to be susceptible to SARS-CoV

How many total cases and deaths have been caused by SARS-CoV-2?

At the current rate, 850k deaths worldwide per year, nearly 700k cases.

What aspect of SARS-CoV-2 transmission made it virtually impossible to control by quarantine?

Asymptomatic individuals could spread the virus unknowingly.

What populations are most vulnerable to COVID-19?

Elderly and those with co-morbidities such as lung problems, diabetes and obesity, cancer and blood disorders, kidney/liver disease, heart disease, and immunocompromised people.

What type of COVID-19 vaccines are most widely distributed across the US?

Pfizer and Moderna are mRNA vaccines--mRNA of spike protein

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Janssen-- viral vectored vaccine, a genetically modified adenovirus carries DNA for COVID-19 spike protein.

What are the common SARS-CoV-2 therapies that were discussed in class? What viral proteins are targets of Molnupiravir and Paxlovid?

Steroids, monoclonal antibodies

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Molnupiravir targets nucleoside analogs

Paxlovid targets protease inhibitors

How are arboviruses acquired? How do they spread?

Acquired by an insect through either vertical transmission or blood meal

Spread through the blood.

What are the 4 vectors that we discussed in class?

1. Mosquito
2. Sandfly
3. Midge
4. Tick

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What is the difference between a reservoir and a non-reservoir host?

Arboviruses do not cause disease in the reservoir host but can cause severe disease in the non-reservoir host.

Why is it virtually impossible to eliminate arboviruses?

Multiple species can spread the virus, it is not isolated into one.

What kind of virus is Yellow Fever Virus? Where does it get its name? Roughly how many people get a severe disease from YFV? What organ is the primary target of YFV? How many people get infected and how many people die per year?

→Yellow Fever Virus is a (+) strand RNA flavivirus

→Gets its name from jaundice that is occasionally associated with the disease caused by the release of bilirubin.

→Liver is the primary target

→ 200k cases, 30k deaths

Be able to explain the difference between the Sylvatic cycle and the Urban cycle of transmission. Which mosquitos provide transmission in each cycle?

→ Sylvatic cycle (transmission between insect to monkey in the jungle): monkey to insect to monkey

→ Urban cycle: mosquito to human to mosquito

→ *Haemagogus* species spreads in the sylvatic cycle

→ *Aedes aegypti* spreads in the urban cycle

What are some of the impacts that YFV has had on society?

* Brought to Americas during years of slave trade
* Most of Napoleans troops died from YFV
* Mexican-American war: more soldiers died from disease than by battle
* 1901--Walter Reed confirmed the route of transmission

Why is YFV less prevalent than other Arboviruses discussed?

Vaccination against YFV gives lifelong protection. YFV still spreads among unvaccinated individuals.

What type of virus is Dengue virus? Where is the virus prevalent? How many people are infected, get severe disease, and die each year from Dengue? What are the ranges of disease caused by Dengue?

* Dengue virus is a Flavivirus
* Prevalent in some Asian and Latin American countries
* \~400 million people infected per year
* 500,000 get severe disease, 2.5% die
* 95% of cases result in asymptomatic or “mild” disease, 5% progresses to more severe, life-threatening fever/shock syndrome

The headaches and muscle aches caused by Dengue have given it the alternate name _______.

“Break-bone fever”

Why is Dengue more severe the 2nd time you get infected?

Antibody-dependent enhancement

What is antibody-dependent enhancement? Describe how this functions to enhance Dengue virus replication. Why does it make vaccine development a nightmare?

Antibodies made against one serotype can cross-react with other serotypes. These antiviruses are unable to neutralize virus of a different serotype.

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Non-neutralizing antibodies recruits macrophages/monocytes to the site of infection; “Trojan horse”

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Virus infects these cells, kills them, and produces even more progeny that are released into the bloodstream.

What type of virus is the Chikungunya virus (CV)? Where was it first identified? Where was the large outbreak that resulted in a rapid increase in the incidence of disease?

* Togaviridae, alphavirus, (+) strand RNA virus
* Identified in Tanzania
* Large outbreak on Reunion Island in the Indian Ocean, 1/3 population infected

What areas are at risk of Chikungunya?

Countries in Africa and Southeast Asia

What is the major symptom of Chikungunya that does not go away?

Symptoms include high fever, nausea, petechial spots, and joint pain. Joint pain does not go away.

What are petechial spots?

Petechial spots are characteristic red spots that appear on the skin.

What type of cells carry CV into the synovial tissue of joints?

Monocytes and macrophages carry CV into synovial tissue of joints.

How did CV enhance its transmission/geographical range following the outbreak on Reunion Island?

CV was originally transmitted by *Aedes aegypti*, but its vector changed to *Aedes albopictus*, result of a single amino acid change in the E1 glycoprotein.

What treatment(s) can be given to address chikungunya disease?

There are no vaccines or therapeutic drugs. Anti-inflammatory drugs reduce pains associated with severe arthritis.

What family of viruses are the measles and mumps viruses in? What type of viruses are they?

Measles and mumps are in the **paramyxoviridae** family and are ssRNA (-) viruses.

How many deaths were attributed to measles globally in 2019?

WHO estimates 207,500 deaths globally in 2019

What is the R0 for measles and what is one reason it spreads so well?

R0 = 12-18, highly transmissible

The airborne virus that maintains viability for up to two hours after an infected person leaves the area. Infections peak in late winter to early spring.

Know the defining features of measle and mumps disease.

* Incubation period: 7-14 days
* Prodromal phase: 2-4 before distinguishing rash, Koplik spots (rash on mucous membranes)
* Begins on the face and upper neck and then spreads to the trunk and limbs.
* Fades in order of appearance

What is immune amnesia and how does it relate to the Measles virus?

* Measles infects memory T and B cells which are dramatically reduced in the host during the acute stage of infection.
* Measles virus infection diminishes preexisting antibodies.
* It can take approximately 2-3 years for protective immune memory to be restored.

What are some complications of Mumps outside of Parotitis?

Parotitis: swelling of the salivary glands and parotid gland

Meningitis, Orchitis (testicular inflammation), Oophoritis (swelling of the ovaries), Encephalitis, Pancreatitis, permanent or transient deafness.

Who developed both the Measles and Mumps vaccines that are currently used in the MMR vaccine?

MMR II→ combination measles, mumps, and rubella vaccine

ProQuad→ combination measles, mumps, rubella, and varicella vaccine.

What are intrinsic resistance factors?

Proteins or RNAs that are **present** in an **uninfected** host that can limit or block virus replication upon detection.

What is apoptosis and how might it restrict virus replication?

**Apoptosis** is programmed cell death. It is a way to destroy the cell before it becomes hostile.

How does apoptosis limit inflammation from a dying cell?

It destroys an infected cell without initiating inflammation.

What is autophagy and how does it restrict virus replication? How do viruses subvert autophagy for their own benefit?

* Autophagy is a mechanism for recycling redundant or damaged cell content


* It can restrict the replication of viruses, bacteria, and parasites, and may inhibit replication at multiple steps of the viral lifecycle.

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What type of species use RNAi for antiviral defense?

Invertebrates and plants

Describe how RNAi works. What are the major cellular factors required for RNAi?

* dsRNA produced during infection is cleaved by DICER into small RNAs of 21-23 nts (termed **small-interfering RNAs**)
* siRNAs are loaded into RISC (RNA-induced silencing complex)
* RISC identifies viral mRNAs containing identical sequences
* **SLICER,** a nuclease in RISC, cleaves viral RNA

What is CRISPR and how does it contribute to immunological memory?

**CRISPR**: Clustered regularly interspaced short palindromic repeat.

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* Bacterial genomes contain loci of repeats and spacers where small fragments of phage genomes (30 bp) are inserted after initial infection.
* Upon reinfection with a phage, these regions are transcribed, along with Cas proteins.
* These RNAs identify the identical sequence in incoming phage and is cleaved by Cas proteins
* As the phage genome fragments are incorporated into the genome, this memory is transferred to subsequent generations.

What is a PAMP and what are some common PAMPs that illicit an innate immune response?

**PAMPs** are pathogen-associating molecular patterns. The cell must be able to detect the pathogen and must identify specific aspects of pathogens that are different from itself.

* dsRNA or ssRNA in the endosomes
* DNA in the cytoplasm or in unique nuclear compartments
* Specific viral proteins

What is a PRR?

**PRRs** are Pathogen Recognition Receptors. They are toll-like receptors, membrane-bound proteins located at the cell surface or in endosomes.

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They bind to a variety of ligands--dsRNA, ssRNA, unmethylated CpG DNA, and bacterial components.

Which PRRs are membrane-bound? Where do they detect PAMPs?

* Toll-like receptors (TLRs) are membrane-bound
* TLRs detect PAMPs in ligand binding domains

Which PRRs detect RNA/DNA in the cytoplasm?

* RIG-I-like receptors (RLRs)
* DDX/DHX receptors (DNA/RNA helicases)
* NOD-like receptors (NLRs)

Describe innate immune signaling starting with a PRR.

* Cytoplasmic, endosomal, and plasma membrane PRRs sense infection


* Activated PRRs recruit specific adaptor molecules and transcription factors that go into the nucleus and initiate transcription of interferon genes (IFN)

What transcription factors drive this response?

Interferons (IFNs)

What is IFN? How does it stimulate the production of ISGs? What transcription factors does it activate?

* IFNs are soluble factors that interfere with virus replication
* IFN is secreted from the cell and binds to its receptor inducing another signaling cascade.
* STAT proteins are phosphorylated which induces translocation into the nucleus
* STAT proteins act as transcription factors to initiate the transcription of genes
* Final result is the production of interferon-stimulated genes or ISGs

Describe the ISGs discussed in the slides

* APOBEC3G→ cytodine deaminase mutates viral DNA
* Zinc-antiviral protein (ZAP) → binds viral RNA at CG dinucleotides and recruits cellular enzymes to degrade it
* Tetherin→ binds to viral particles and prevents their release
* IFITM3→ Transmembrane protein that blocks entry of enveloped viruses
* Ly6E→ Prevents membrane fusion of enveloped viruses
* TRIM5α→ inhibits HIV uncoating
* CXCL-10→ recruits T-cells to site of infection.

What are the differences between adaptive and innate immunity? How do they work together to create an effective response to pathogens?

* Adaptive immunity→ general features of pathogens, short-lived effects
* Innate immunity→ very specific and long lasting
* Innate cytokines recruit adaptive cells to the site of infection and activate them
* Adaptive cells help enhance the activity of innate cells

What are the major cells of the adaptive immune response?

Lymphocytes (T and B cells)

What is an antigen? What types of molecules can serve as antigens?

* Antigens are molecules that are recognized by T and B cells.
* Sugars, lipids, nucleotides, and other chemicals can serve as antigens

What is an epitope? Can an antigen have more than one epitope? How are epitopes created?

* An epitope is the segment of a molecule that is recognized by T or B cells
* An antigen **can** have more than one epitope
* Epitopes are created by the degeneration of proteins during infection into small peptides

What are the proteins on T cells and B cells that recognize epitopes?

* T cells→ T cell receptor (TCR)
* B cells→ B cell receptor (BRC)

What type of protein must an epitope be displayed on for recognition?

Major histocompatibility complex protein, or MHC

What are the types of MHC molecules"? Which types of cells can present MHC molecules?

* Two types, MHC I and MHC II
* All nucleated cells express MHC I
* Only dendritic cells and B cells express MHC II
* DCs and B cells are considered “antigen-presenting cells” or APCs.
* MHC I and MHC II can present to TCR

Only MHC II can present to BCR

What are the genetic methods used to create unique T/B cell receptors?

→Imprecise recombination

→ Alternative splicing after transcription

→ Hypermutation of TCR/BCR to develop tighter binding

→Broad diversity of T and B cell receptors

What are helper T cells, and how do they provide “help” to other immune cells?

* Also known as CD4+ T helper cells, are a subset of T cells that provide help to initiate the adaptive immune response
* TCR of naïve TH cells bind to epitopes by APCs
* Only interact through MHCII

How do TH cells differentiate into TH1 and TH2 cells?

Dependent on the cytokines present at the time.

* IFNγ→ TH1
* IL4→ TH2

How does cell-mediated immunity kill virus infected cells?

* CD8+ cytotoxic T cells are activated by cytokines produced by CD4 TH1 cells.
* Also have TCR that recognizes epitopes, only recognize those bound to MHC-1
* Peptides presented on MHC-1 are produced inside the cell as a result of virus infection

What is “humoral” immunity?

Humoral immunity is initiated when B cells are stimulated by cytokines secreted by TH2 cells.

Membrane-bound antibodies bind to their specific epitope and move to the nearest lymph node, undergoing clonal expansion→ become memory cells

Circulate in the serum

What are the features of antibodies?

Y-shaped molecules made of two heavy chains and two light chains (Fab and Fc regions)

What are the differences between different antibody isotypes?

* The order in which they appear
* Location in the body where they act
* Whether they are monomeric or multimeric

What are the ways in which the antibodies inhibit viral replication?

* Bind virus or pathogen with the Fab region
* Prevent it from entering new cells or locations
* Can also enter cells with virus and prevent uncoating

What are some mechanisms used by viruses to evade adaptive immunity?

* Mutate the epitope
* Prevent transport/loading of MHC-1 molecules
* Produce large amounts of secreted antigenic protein that is not important for replication or pathogenesis
* Encode for “decoy” cytokines
* Utilize cell-to-cell spread and limit amount of time virus is exposed to antibodies.