Module 3 Exam

Virus

Tiny infectious agents, obligate intracellular parasites, must have a host, no organelles, no cytoplasm, no cell nucleus, acellular, protein coat and nucleic acids, abundant

virion

inert particle that does not carry out metabolism or energy consumption; ready, complete, intact

prophage

a virus that has integrated their genome into the bacterial genome

provirus

a virus that has integrated their genome into a human cell

endogenous virus

a permanently integrated provirus transmitted via the germ line

naked virus

virus composed of only a nucleocapsid, some capsid proteins are spikes that help the virus attach to and penetrate the host cell

envelope

flexible, membraneous layer of a virus

\-proteins extend as spikes

Group I

**Genome: Ds DNA**

mRNA template: DNA (+/-)

mRNA produced in: nucleus

Polymerase used to synthesize mRNA: DNAd RNA pol

Genome template: DNA (+/-)

Polymerase used to synthesize genome: DNAd DNA pol

Group II

**Genome: ss DNA**

mRNA template: DNA (+/-)

mRNA produced in: nucleus

Polymerase used to synthesize mRNA: DNAd RNA pol

Genome template: DNA (+/-)

Polymerase used to synthesize genome: DNAd DNA pol

Group III

Genome: Ds RNA

mRNA template: RNA (+/-)

mRNA produced in: nucleus

Polymerase used to synthesize mRNA: RNAd RNA pol

Genome template: RNA (+/-)

Polymerase used to synthesize genome: RNAd RNA pol

Group IV

Genome: (+) ss RNA

mRNA template: RNA (-)

mRNA produced in: cytoplasm

Polymerase used to synthesize mRNA: RNAd RNA pol

Genome template: (-) RNA

Polymerase used to synthesize genome: RNAd RNA pol

Group V

Genome: (-) ssRNA

mRNA template: (+) RNA

mRNA produced in: cytoplasm

Polymerase used to synthesize mRNA: RNAd RNA pol

Genome template: (+) RNA

Polymerase used to synthesize genome: RNAs RNA pol

Group VI

**Genome: (+) RNA**

mRNA template: (-) RNA

mRNA produced in: nucleus

Polymerase used to synthesize mRNA: reverse transcriptase

Genome template: (-) RNA

Polymerase used to synthesize genome: DNAd RNA pol

\*\*RNA retrovirus

Group VII

DNA pararetrovirus

Virus shape

characteristic of virus that is determined by either its capsid or its nucleic acid

Icosahedral virus

identical subunits that make up equilateral triangles fused together in a spherical shape

\-genetic material fully enclosed

Helical Virus

The capsid consists of a long tube of protein, with the genome coiled inside

• vary in length, depending on genome size

• commonly used by plants

Complex viruses

have an icosahedral “head” and helical “neck”

Asymetrical virions

viruses that lack capsid symmetry

* ex. influenze viruses (RNA virus)

Generic viral replication

1. Attachment to the host

   1. using spikes

2. Entry into cell and uncoating genome

   1. fusion/endocytic event occurs → engulfs cell

   2. capsid breaks apart

3. Gene expression and protein production

   1. Baltimore classification

4. Assembly and Exit from cell

Tissue tropism

tissues of a host that support growth of a particular virus or bacteria (due to recognition of particular receptors

ex. influenza virus normally infects lung tissue but not brain tissue

Cellular tropism

cells of a host that support growth of a particular virus or bacteria (due to recognition of particular receptors)

ex. HIV normally infects macrophages but not neurons

Host tropism

the infection specificity of certain pathogens to particular hosts and host tissues (due to recognition of particular receptors)

ex. Myxoma virus normally infects rabbits but not humans

Fusion

\

Endocytosis of non-enveloped virus

Endocytosis of enveloped virus

Injection of nucleic acid

\+RNA viruses

the genome is mRNA

ex. rubella, west nile, HepA, HepC

\-RNA viruses

Influenza, rubeola, Mumps, Hantavirus

Viral Exit

Release of progeny viruses from host cell

• lysis of cell

• budding

Influenza

Family: Orthomyxoviridae

Baltimore Class V

Usually round - asymmetrical

Enveloped

Influenza Genome

Segmented (8 segments)

• Codes for 12-14 proteins depending on strain

• PB1, PB2, PA code for RNA pol

MI

codes for matrix proteins (influenza)

HA

part of spike protein involved in attachment (influenza)

NA

part of spike protein involved in egress (influenza)

Influenza A

wide host range (broad tropism)

“misery” -- very sick

Bird flu

Influenza B

infects seals, humans, ferrets

\-mutates more slowly

\-mild infection

Influenza C

infects humans, dogs, pigs

\-No HA/NA

\- Instead HEF

Influenza D

infects swine, cattle, sheep, goats

\-Bovine influenza virus

Influenza attachment

Interaction occurs between H spike and Sialic acid

• Humans: 2:6 sialic acid linkage

• Birds: 2:3 sialic acid linkage

• Pigs: both sialic acid linkages

Influenza entry and uncoating

1. H-S interaction

2. Host cell invaginates virus H→ F (fusion)

3. Uncoated genetic material released into cytoplasm

   1. acidic environment breaks down

Nucleus

Uncoated genome and polymerases move into the ____ (influenza)

Cap snatching

• the process of obtaining a 5’ cap by taking it from a host mRNA

• resulting progeny are all capped

• cap used for recognition by ribsome

• reason why virus goes into nucleus

• Influenza genome**

Replication cycle of influenza A

• Viral mRNA returns to cytoplasm for translation

• (+) strand RNA synthesized by RdRp

• Assembly occurs in cytoplasm'

• envelope proteins synthesized at the ER then glycosylated and transferred to the Golgi for export to the cell membrane

• At membrane, packaged (-) RNA segments are enveloped by host membrane containing the envelope proteins

• Mature virions bud out of cell membrane

Antigenic Drift

The influenza virus continually acquires small mutations that can lead to new phenotypes with respect to drug resistance and host range

• small changes over time

• like evolution

• changes in specific receptors

• gradual in time and intensity

• ex. annual flu shot → virus changes slightly each year

Antigenic Shift

• very sudden changes over time

• short period of time

• very dramatic in time and intensity

• example: pig can get bird and human flu→ reassortment into a combination of both

Tamiflu

influenza treatment that works by inhibiting neuraminidase activity

→ inability to cleave receptor = virion stuck to host cell surface = no virion release = recognized by immune system and destroyed

Bacteriophages

viruses that infect and parasitize bacteria

• inject only their genome into a cell through the cell envelope

• its capsid (“ghost”) remains attached to cell surface

Lambda phage

bacteriophage that binds to E. coli by contact between its tail fibers and the maltose porin

* icosahedral head

Lytic cell

• bacteriophage replication that generates large numbers of progeny

• lyse the host cell

• all bacteriophages capable of this

Lysogenic cycle

• Bacteriopage is quiescent

• integrates as prophage

• can reactivate to become lytic

• virus can acquire host genes and pass them onto other host cell via transduction

cI

protein that encodes for a repressor protein that blocks cro promoter

• represses lytic cycle

• activates lytic cycle

• is cleaved by RecA (activated by DNA damage)

Cro

protein that activates lytic cycle and represses lysogenic

viroids

the smallest known pathogens, infectious RNA particles

• cause disease in crop plants (apple scar skin)

• do not contain genes and do not produce proteins

• Highly complementary, circular, single-stranded RNA molecules

Hepatitis D

a ss (-) sense RNA

• requires Hep B for infectivity (not virus, codes for gene)

• Replicates in the nucleus of liver cells

Prions

• proteinaceous infectious particles

• contains no DNA

• contains no RNA

• Composed entirely of protein (PrP)

• Transmissible from animal to animal (infectious)

• Can develop spontaneously

• Can be inherited

Human Prion Disease

• Human Creutzfeldt-Jakob Disease (CJD) -Spontaneous

• Variant CJD (vCJD) - acquired

• Kuru-acquired

Creutzfeldt-Jakob Disease

• Sporadic (85% cases)

  • occurs spontaneously (1 in a million)

  • most cases

  • age 60 in common

• Heredity (15%)

  • 10% are inherited mutations

• Acquired (less than 5% of cases) -vCJD/Kuru

  • exposure to contaminated brain or nervous tissue

Animal Prion disease

Bovine Spongiform Encephalopathy (Mad Cow Disease)

• Chronic Wasting Disease

• Mule deer, white tailed deer, elk moose

Scrapie-→ Sheep

PrPc

\-pre-prion proteins

\- normal cellular protein

\-Mainly alpha helices

\-readily digested by proteases

\-involved in cell-cell communication in the brain

PrPsc

\-sc=scrapie (1st identified)

\-converts normal proteins to infectious proteins

→ induces abnormal folding of cellular proteins found in the brain

\-primarily B-pleated sheets

\-Highly stable

\-Resistant to proteases and UV light

Ebola

Filovirus in the Family Filoviridae

\-Pleomorphic (6 or U (filamentous))

\-Enveloped

\-Single-stranded negative sense RNA

\-zoonotic

Ebola Transmission

Direct contact with body fluids:

• Blood

• Vomit

• Urine

• Fecal matter

• Sweat

• Spit

• Semen

• Objects contaminated w virus

• Infected animals (body fluids or animal meat)

*only spread after symptoms begin

*2-21 days after exposure (8-10 days most common)

*Generally death occurs between day 6 and 16

Ebola attachment

-surface gp binds to host receptors (DC-SINE)

• Macrophages, dendritic cells, endothelial cells

• Important for virus detection and immune response

Macropinocytosis

an endocytic event in which the plasma membrane protrudes (actin filaments) and captures virus in a vesicle, forming macropinosome that enters host cell → fuses to endosome

\-Entry of Ebola; same strategy apoptotic cells use

\-Silent entry (doesn’t trigger IS)

Ebola Genome

-18-19 kb genome, encodes for 7 proteins

• VP-35: prevents host antiviral signaling

• VP30: indicates transcription

• vp24: counters host innate immunity

• NP: replication and assembly

• VP40: regulates assembly and egress

Malaria

Regions with Increased ebola rates → increased ___ rates

• Plasmodium: given through malaria

• Correlation to plasmodium count and ebola survival rate

• No treatment for Ebola (cure)

Humman Immunodeficiency Virus

Genus Lentivirus and Family Retroviridae

\-Baltimore class VI

\-enveloped

\-icosahedral

\-capsid: contains 2 ss RNA genomes

\-genetically “diploid”

\-5’ cap and 3’ poly A tail

CD4

-HIV particles enter only if virions bind to ____

• Gp120 (SU)

• Gp 42 (TM)

Fusion Event

Hiv interaction of CD4 (found on helper T cells) and gp120

Reverse transcriptase

\-RNA dependent cDNA polymerase (cDNA = complement of RNA genome)

\-needs a free primer or free 3’OH

\-RNAse H activity (like DNA pol I → removes primer)

\-Also acts as a DNA dependent DNA polymerase also

\-Error prone enzyme (1-2 errors per copy)→ makes HIV hard to treat

tRNA

has a free 3’ OH which gets used as a primer by DNA polymerase (in reverse transcription)

Integrase

trims 2 nucleotides from each 3’ end of viral DNA

cleaves host DNA at an integration site

Accessibility of DNA influences sites of integration (ex. hot spots)

Ligase

___ activity covalently bonds viral DNA to host DNA

Vpu

Viral protein required for egress of HIV; digests tetherin (holds virus to host cell)

non-nucleoside reverse transcriptase inhibitors (NNRTIs)

HIV treatment that binds to reverse transcriptase to inhibit it

* Sustine

nucleoside reverse transcriptase inhibitors (NRTIs)

molecules that look like nucleotides get incorporated into DNA, reverse transcriptase can’t go faster because no complements to the “bases” exist

* Truvada

Protease inhibitors (PIs)

HIV Treatment that stops the cleavage of proteins

* Lexiva

Entry or fusion inhibitors

HIV treatment that prevents entry of HIV virus

* Fuzeon

Integrase Inhibitors

HIV treatment that inhibits Integrase activity

* Isentress

CCR5 antagonists

HIV treatment that inhibits a necessary co-receptor (CCR5)

* Maraviroc

Atripla

Current best recommended treatment for HIV

• Efravirenz/tenofovir/emtricitabine

• targets reverse transcriptase

HIV transmission

Unprotected sex, unprotected oral sex, contaminated needle stick, blood transfusions or organ/tissue transplants, eating food pre-chewed by HIV infected person, bitten by HIV infected, deep mouth kissing w/ bleeding gums (very descriptive candice…)

* Mother → child: pregnancy, labor, delivery, breast-feeding

Coronavirus

\-Group IV, enveloped virus

\-Zoonotic

\-Helical genome

\-125 nm

\-Characteristic spikes

\-Genome has 5’ cap and poly A tail

SARS-CoV-2

Severe acute respiratory syndrome-Coronavirus-2

\-causes Covid-19

\-Similar to the SARS virus that caused 2002 outbreak

\-similar to the MERS virus that caused the 2012 outbreak

ACE-2 (Angiotensin converting enzyme-2)

The specific receptor on the surface of host cells that coronavirus spike protein binds to

• Low levels in kids

• High levels in adults

Angiotensin converting enzyme-2

Coronavirus Attachment

1. S proteins bind to the ACE-2 receptors on surface of lung cells

   1. pre-binding spike must change shape to expose RBD (part that interacts with ACE-2)

2. Serine protease (TMPRSS2) binds and cleaves the ACE-2 receptor, activating the spike

3. Cleaved ACE-2 and activated spike protein facilitate viral entry

RBD

The specific part of the S protein that interacts with ACE-2 (Coronavirus)

• switches between a lying down(immune invasion) to standing up (receptor binding) position… activated by furin

• where many mutations occur in SARS-CoV-2

• ability to bind affects pathogenicity (selective pressure)

Endocytosis

Method of entry for SARS-CoV-2

\-S protein is cleaved by endosomal proteases to activate its fusion activity

\-viral membrane fuses with the endosome membrane → releases genome

Biosynthesis

SARS-CoV-2: all in cytoplasm

1. Membrane fusion and viral RNA release

2. Translation

3. Proteolysis

4. Transcription

5. 5a. RNA replication and packaging

6. 5b. Translation

7. Assembly and budding

8. Exit via exocytosis

Exocytosis

Method of exit for SARS-CoV-2

1. Buds out of ER

2. Fuses with golgi body

3. Takes golgi membrane (like cell membrane)

4. Buds out of golgi

5. leaves via ___

Long-Covid

Phenomenon that there is residual COVID that’s hiding in body, evading immune system; or covid impacts the immune system (decreasing T cell count)

* Long term health implications include brain fog, shortness of breath, Heart arrhythmia, and Hypertension

toll-like receptors

Receptors responsible for immune response to SARS-CoV-2

* Bind LPS, Lipopeptides, Flagellin

IFNs

___ induce expression of enzymes that block viral replication

3 key outcomes:

1. inhibition of viral protein synthesis

2. Degradation of viral RNA

3. Inhibition of viral gene expression and virion assembly

ORFs

nonstructural proteins responsible for anti-immune response → inhibit IFN signaling

Lung tissue damage

_____ often occurs in covid patients because macrophages are trying to kill virus and damage residual tissue

memory cells

allow the immune system to respond more efficiently/effectively by being able to recognize previous pathogens when they reappear

\-purpose of vaccines

\-not working well with SARS-CoV-2

cytokine

broad category of proteins that are responsible for communication

cytokine storm

A severe immune reaction in which the body releases too many cytokines into the blood too quickly

\-triggered by covid-19

\-can result in multi-organ failure and death

immunology

scientific study of how the immune system functions in the body to prevent or destroy foreign material