exam 3

virology: ch 13, 20.6 &27 (HIV/AIDS sections only)

what family is SARS-COV-2?

Beta Corona Virus

is SARS-COV-2 enveloped or unenveloped?

enveloped

what is a unique feature of SARS-COV-2

it contains a unique spike glycoprotein that gives allows it to invade other cells, specifically, those containing the ACE2 receptor

where can ACE2 be found in the human body?

human ACE2 receptors are commonly found in the epithelium cells in the respiratory and digestive tract

what organ does SARS-COV-2 target + outcome

COVID-19 primarily goes after the respiratory system, where ACE2 receptors on cells are predominant. the virus replicates in the respiratory tract. once it makes it way to the lungs, the virus can cause apoptosis of infected pneumocytes, spread alveolar damage, weaken and cause capillaries to leak, and impair gas exchange

4 COVID-19 omicron + variants characteristics

1. higher transmission (more infectious)

2. decrease in people losing sense of taste/smell

3. vaccinated population is more likely to experience symptoms

4. less likely to cause severe symptoms

what tests are used for current covid-19 infections?

1. RT-PCR: most accurate because it detects RNA genome of virus using reverse transcriptase (RNA → DNA) and amplifies DNA for detection

2. Antigen test: detects viral proteins using ELISA, false results may show up when low levels of virus (early stages of infection) are present.

covid-19 test used for previous covid-19 infections

antibody tests: use the ELISA format to detect antibodies against covid-19, highly specific and results indicate if you were previously infected because antibodies take a while to develop

regeneron

“cocktail” treatment used against early stages of covid-19 infection. contains monoclonal antibodies that work against the spike protein

paxlovid

pfizer: oral antiviral obtained through prescription that inhibits viral replication prior to severe symptoms/disease of covid-19

molnupiravir

merck: oral antiviral prescribed to pt w/ covid-19 before severe symptoms/disease, works by causing RNA to mutate

how do mRNA vaccines work against covid-19

vaccines cause human cells to express spike so that the immune system develops anti-spike Ab

• pfizer and moderna

how do new variants impact vaccine efficacy?

variants often contain mutations and changes to spike proteins that the antibodies developed by the vaccine cannot recognize

what are some general characteristics of viruses

viruses are non-living entities and can infect all lifeforms, they are commonly referred to by the organism they infect (bacteriophage). viruses are also self assembling

T/F: viruses are organisms

false

viruses are technically not considered to be ‘alive’ bc they cannot live/replicate independently w/o a host cell. viruses are just nucleic acid surrounded by protein and lack organelles

virion

a virus particle consisting of nucleic acid surrounded by capsid

naked virion

do not have envelope

enveloped virion

surrounded by lipid membrane, may contain matrix proteins, only found in eukaryotic viruses

capsid

protein coat made of capsomers that enclose nucleic acid

icosahedral symmetry

most common virus shape, contains 20 isometric (equilateral flat surfaces)

pleomorphic/complex viruses

most phages are this kind with an isometric head + long helical sheath/tail and helical or rod like appearance in the virion

nucleocapsid

viral capsid together w/ nucleic acid that is packed w/n protein coat

what do attachment proteins/spikes and tail fibers do

mediate attachment to the host

do viruses contain RNA and DNA?

no, they either contain DNA or RNA, not both

what is the structure or viral genomes?

linear or circular and can be single or double stranded

what do viral genomes encode for?

• viral protein coat

• assure replication of viral nucleic acid

• movement in/out of host

• enzymes not present in infected cell

viruses in the extracellular phase are metabolically ______

inert

viruses in the intracellular phase are metabolically ______

active

lytic cycle

phage lyses host cell and takes over metabolic processes of cell

non-lytic cycle

phage extrudes out of infected cell (filamentous phages) and only partially take over cellular metabolic processes

lysogen

bacteria carrying viral DNA

lysogenic state

virus is integrated into chromosomes/DNA of hose and replicates w/ it, also called temperate phages

lysogenic conversion

viral DNA modifies properties of bacterium- toxin production

what are the 6 stages of lytic cycle?

• attachment/adsorption

• penetration

• replication

• assembly/maturation

• release

attachment

protein fibers located at the end of the phage’s tail attach to specific receptors on the host cell’s cell wall

penetration (plant/bacteria viruses)

phage injects nucleic acid into host cell through the cell wall by degrading portion of cell wall to create a hole using lysosyme, phage coat remains outside cell

penetration (animal viruses)

entire phage is able to go through cell wall since animal cells lack rigidity and is engulfed by the cell via phagocytosis and go into uncoating step to release nucleic acid from capsid

• enveloped viruses: undergo membrane fusion and fuse to the plasma membrane of the host cell to phage’s envelope

transcription

phage DNA is transcribed into mRNA and then proteins

replication

new copies of phage particles are produced and protein. is synthesized

in this stage the phage will also inhibit activity of the host DNA by producing enzymes to destroy host DNA

assembly/maturation

DNA is packaged in phage head protein and components come together to form matura phage

release

intracellular phages release enzyme to digest host cell wall (cell becomes lysed) and viruses are released

• eukaryotic/animal viruses: as phages leave host cell, envelope is picked up as envelope is made of a portion of host cell plasma membrane and becomes lipid envelope of virus

lytic ssRNA phages

MS2, Qβ

only infect F+ strains of E.coli and attach to the sides of sex pilus, replicate rapidly (~ 10,000) and requires RNA dependent RNA polymerase that must be encoded on entering phage RNA

phage λ (lambda)

most phages 90% temperate phages and can occur is slow growing bacteria and become prophage

e.coli phage that binds to very specific spot in host DNA strand (homologous match")

prophage

integrated phage DNA

lysogenic cell/lysogen

bacterial cell carrying prophage

lysogenic conversion

phage DNA codes for proteins that modify cell properties

what is the difference between the lytic and lysogenic cycle?

in the lysogenic cycle, the phage DNA is not immediately transcribed and replicated like in the second stage of the lytic cycle. instead, the viral nucleic acid integrates itself into a specific part of the host’s chromosome. the host continues to replicate with the phage’s DNA, passing it onto progeny. this occurs until induction

induction

step in lysogenic cycle where host cell is exposed to UV or a chemical (from a lab) that ‘activates’ phage DNA to excise and enter lytic cycle as normal

phage repressor

binds to phage operator to inhibit expression of excision and lysis genes, also inhibits infection of cell w/ phage of the same type and replication

if repressor stops being made or is inactivated, excisase is produced = phage DNA excises, reproduces and lyses cell

ssDNA filamentous phages

infect only F+ strains of E.coli and attach to tip of sex pilus. phages go inside of cells and just replicate, they do not lyse the cell

transduction

DNA is transferred from one bacterial cell (donor) to another (recipient). can sometimes encode resistance genes

generalized transduction

via generalized transducing phages- virulent and temperate phages. can be any gene of donor cell. transducing phage is defective bc it lacks viral DNA necessary to form complete phage and lyse recipient cell

specialized transduction

via specialized transducing phages- only temperate phages. transfer only a few specific genes

host ranges

number of different bacteria a phage can infect

limiting factors to hose ranges

• host receptors: most phages are specific, ex: phage lambda only infects E.coli

• must overcome host restriction modification system

alteration of host cell receptors

• mutation

• lysogenized bacteria can alter cell surface resulting in alteration of receptor site

restriction modification system

1. restriction enzyme: codes for endonuclease, cuts small segments of viral DNA when recognized

2. modification enzyme: attaches methyl group to DNA flagged by restriction and will not be recognized later on, protecting cell’s own DNA

phage therapy

use of bacteriophages as antibacterials to treat pts

phage lysins as antimicrobials

use of phage enzymes to treat infections as opposed to whole phage

CRISPR

clusters of regularly interspersed short palindromic repeats

phage spacer DNA inserted into CRISPR, providing record of infection. small RNAs bind to Cas (CRISPR associated sequences) proteins and bind spacer RNA to phage, targeting phage for destruction

enteric viruses

generally fecal-oral transmitted, often cause gastroenteritis, some cause systemic disease

respiratory viruses

transmitted via droplet, generally localized in respiratory tract

zoonotic viruses

transmitted via animal → human via animal vector

sexually transmitted viruses

can cause genital lesions or systemic infections

herpesviridae

herpe simplex: enveloped, double stranded DNA virus

hepadnaviridae

hepatitis B: enveloped, double stranded DNA virus

papillomaviridae

HPV: non-enveloped, double stranded circular DNA

polyomaviridae

non-enveloped, double stranded circular DNA

adenoviridae

cold, conjunctivitis: non-enveloped, double stranded linear DNA virus

parvoviridae

canine parvo: non-enveloped, single stranded DNA virus

poxviridae

smallpox: enveloped, complex DNA virus

flaviviridae

dengue/zika: enveloped, icosahedral, positive sense, single stranded RNA virus

togaviridae

enveloped, icosahedral, positive sense, single stranded RNA virus

retroviridae

HIV: enveloped, icosahedral, positive sense, single stranded RNA virus

*replicates in nucleus

coronaviridae

SARS COV2: enveloped, helical, positive sense single stranded RNA virus

picornaviridae

common cold: non-enveloped, icosahedral, positive sense, single stranded RNA virus

caliciviridae

non-enveloped, icosahedral, positive sense, single stranded RNA virus

orthomyxoviridae

influeza: enveloped, helical, negative sense, single stranded RNA virus

*replicates in nucleus

paramyxoviridae

measles: enveloped, helical, negative sense, single stranded RNA virus

rhabdomyxoviridae

enveloped, helical, negative sense, single stranded RNA virus

filoviridae

ebola: enveloped, helical, negative sense, single stranded RNA virus

bunyaviridae

enveloped, helical, negative sense, single stranded RNA virus

arenaviridae

enveloped, helical, negative sense, single stranded RNA virus

reoviridae

rotavirus: non-enveloped, icosahedral, negative sense, double stranded RNA virus

acute infections

short lived infections, produce large number of viruses during infection (productive)

ex: covid-19, flu, cold

persistent infection

host never really gets rid of virus, may remain dormant (latent), active (chronic), or slow

latent infections

periods of no virus (asymptomatic) and reactivate later

ex: HSV-1 (herpes) - on/off resurgence of sores activated by stress. virus binds to nerves along posterior cervical region and travel down to ‘active sites’ (mouth, genitalia), revealing sores

chickenpox- shingles reactivates chickenpox

chronic infections

symptoms always present due to constant high levels of virus

ex: HBV

slow infections

virus replicates over long period of time, presenting dieases “late”

ex: HIV

first mechanism of enveloped viruses

1. Virion attached to host cell receptors w/ specific protein spikes

2. Viral envelope fuses w/ host cell plasma membrane 

3. Viral nucleocapsid is released directly into cytoplasm 

4. Nucleic acid separates from protein coat (capsid)

second mechanism of enveloped viruses

1. Enveloped virus adsorps into host cell w/ specific proteins 

2. Virion taken in to cell via endocytosis 

3. Host cell plasma membrane surrounds entire virion- forming a vesicle 

4. Envelope of virion fuses with plasma membrane, pH needs to be lowered 

5. Nucleocapsid is released into cytoplasm 

6. Capsid is removed, releasing viral nucleic acid

naked virus mechanism

1. Enters cell via endocytosis, does not fuse with plasma membrane

2. Viral nucleic acid is released from endocytic vesicle by dissolving it 

3. Nucleic acid separates itself from capsid

viral growth cycle

1. attachment + penetration of parental virion; endocytosis → membrane fusion → vesicle escape (naked virus)

2. uncoating of viral genome; nucleic acid released into cytoplasm or nucleus

3. early viral mRNA + protein synthesis; early proteins (enzymes) used to replicate viral genome

4. viral genome replication

5. late mRNA + protein synthesis; structural, capsid proteins

6. progeny assembly

7. virions released from cell

⊕ stranded RNA virus replication

make proteins immediately upon entering host cell, requires ⊖ template strand, occurs in cytosol

⊖ stranded RNA virus replication

go through intermediate for both to make new viruses, occurs in cytosol

DNA virus replication

HAVE to get inside nucleus to replicate, transcription machinery creates messages that are relayed in/out cytosol for proteins to make replicates

viral mRNAs contain

• methylated GTP cap

• poly A tail

• mRNA generated by splicing

how do some viruses make more than one type of RNA from one piece of DNA?

shifting of reading frame

temporal control of transcription from DNA viruses

repressor protein prevents/postpones transcription of some genes