ch13 - viruses, viroids, prions

viruses, viroids, prions

non-living elements

called agents

• not organisms, acellular, no metabolic processes

• virion: complete, infectious virus particle

• viroid: infectious RNA

• prion: infectious protein

viruses: obligate intracellular parasites

• needs to be inside a host cell in order to replicate so they can be transmitted to other hosts

• uses host machinery to replicate

• inactive outside of host

• bacteriophage/or just phage: virus that infects bacteria

general characteristics of viruses

viral structures

• nucleic acid surrounded by a protein coat (capsid)

  • DNA or RNA

• envelope: lipid bilayer outside of capsid

  • naked virus with no envelope

  • enveloped virus

• spikes: proteins on the surface of envelope

  • adherence: helps the virus attach to host cells by binding to receptors

  • causes immunological response by host

    • spikes act as antigens because the immune system recognizes them as foreign

    • they can stimulate the body to produce antibodies that specifically recognize and bind to those spikes

three shapes

• icosahedral

  • triangular

• helical

  • cylindrical

• complex

  • nucleocapsid: dna/rna + capsid

  • tail

  • base plate

  • tail spikes, tail fibers

    • allow for the virus to attach to host cell

10-100x smaller than bacteria

• smallest

  • ~10nm

  • ~10genes

• largest

  • ~800nm

can infect all life forms

• host range: number of different hosts that a virus can infect

  • usually limited to a single species of organism for a single virus

    • ex. some viruses can only infect humans and not animals, some can only infect e. coli, some can only infect certain strains of e. coli

• host range limited by:

  • absence of viral attachment (receptor) site on host cell surface

  • only the cells that have the receptors for the viruses → only affect those specific organs

  • restriction-modification system in host cell - virus must overcome to infect

    • restriction enzymes to cut up the dna of that virus

    • if you have a bacterial cell and the restriction enzymes cut and destroyed the dna, the virus can’t infect it so its a form of protection for the bacterial cell

methods used to study bacteriophages

viruses multiply only inside suitable living cell

1. bacteria: plaque method

• bacteriophages form plaques on a lawn of bacteria

• number of phages determined by counting plaques (PFU)

• will infect all the cells around it

• as it infects all the surrounding cells and produces a lot of viruses it will kill the cells in the surrounding area

• the clearing is full of viruses

2. animal viruses grown in:

• living animals (mice, rabbits, pigs)

• embryonated eggs

  • flu vaccine

3. cell culture or tissue culture

• human cells

replication cycles overview

• use the host machinery to reproduce after infection

1. lytic cycle

• phages multiply inside a cell

• phage lyses cell to release virions (complete virus particles)

• host cell dies immediately, releasing newly formed viruses

2. lysogenic state

• phage dna integrates its genome into the host genome

  • when the dna gets into the host cell it is inserted into the chromosome of the host cell so it becomes a part of the chromosome of the host cell

• the host cell remains alive and copies the prophage when it replicates its DNA

• lysogenic = viral DNA lies low inside the host

• lytic = host cell lyses (bursts open)

the lytic cycle

five step process

1. attachment

• adsorption

• phage attaches to specific receptors on the E. coli cell wall

2. penetration

• genome entry

• the only thing that goes into the cell is the nucleic acid

• the tail contracts and phage DNA is injected into the bacterial cell, leaving the phage coat outside

3. synthesis

• make all the different parts of the virus

• nucleic replication: replicates viral genome

• transcription/translation: synthesis of viral protein coat, spikes, etc.

• some phage genes are quickly expressed

• a phage-encoded enzyme degrades host DNA

• phage DNA is replicated and other virion components are made

4. assembly (or maturation)

• phage components are assembled into mature virions

5. release

• burst size of T4 is ~200

  • number of virions that can be produced per infected host cell

  • each bacterial cell infected with T4 can produce approx. 200 new virions (actual number can vary)

• the bacterial cell lyses and many new infectious virions are released

the lysogenic cycle

replication of a temperate virus

• can undergo lytic or lysogenic cycle

steps of lysogenic cycle

1. attachment

• phage attaches to bacterium

2. penetration

• injected linear phage DNA circularizes and enters lytic or lysogenic cycle

3. incorporation of viral DNA into host chromosome

• reverse transcriptase (RNA → DNA)

• integrase: inserts viral DNA into host genome

  • HIV does this because it’s an RNA virus

• virus is called a prophage (provirus in eukaryotic cells)

• prophage is integrated into the bacterial chromosome

4. viral DNA is replicated when the host cell replicates

• cell division

5. prophage can excise out and undergo lytic cycle

or it can go directly to lytic infection

• after injected linear phage DNA circularizes and enters lytic cycle

• replication of phage DNA and synthesis of phage-encoded proteins

• cells lyse, releasing new phage

effect of viral infection on host cells

host cell immune to superinfection (infection by same phage)

transduction can occur: horizontal transfer of bacterial genes

lysogenic (phage) conversion can occur

• prophages confer new properties on cell → organism displays new trait (expression of phage genes)

• host cells exhibit new traits as a result of being infected with or containing the viral dna

• unfortunately, some of the abilities are to cause disease

• clostridium botulinum: normally it wouldn’t be able to produce botulinum, but when the virus gives the gene to cause disease then it does

• if they were not infected by the virus they wouldnt be able to cause disease

diagnosing viral infections

determined more by patient symptoms

diagnostic tests include

• culturing the virus

• detecting a virus by

  • molecular techniques (PCR)

  • electron microscopy

  • injection into animal → antibodies to virus

animal viruses

classified based on route of transmission for disease-causing viruses

• enteric viruses, zoonotic viruses, respiratory viruses, sxually transmitted viruses

animal viruses - enteric viruses

transmitted via fecal-oral route

cause gastroenteritis; some can cause systemic disease

norovirus, rotavirus

polio can infect the CNS, damage motor neurons and potentially cause muscle weakness or paralysis

animal viruses - respiratory viruses

usually inhaled via infected respiratory droplets

generally, remain localized in respiratory tract

SARS-Cov-2, influenza

can cause more severe diseases when it goes to lower respiratory tract

animal viruses - zoonotic viruses

transmitted from animal to human

rabies, HIV

animal viruses - sxually transmitted viruses

transmitted by sxual activities

can cause lesions on genitalia only or systemic infections

HIV (becomes systemic because it spreads through the blood and infects immune cells), herpes, simplex virus

animal virus replication

five-step infection cycle

• attachment

• entry and uncoating: fusion or endocytosis

• synthesis

• assembly

• release

  • budding: enveloped (lipid bilayer) virus leaves the cell

  • lysing cell

categories of animal virus infections

outcome of infection of eukaryotic cells depends on host defense

• acute infection

• persistent infection

• some viruses exhibit both (HIV)

animal virus infections - acute infections

rapid onset, usually short in duration, more severe

large number of viruses produced

• disease symptoms due to tissue damage (cell death)

host develop immunity (short or long-lasting)

animal virus infections - persistent infections

continue for years or a lifetime

viruses are always present in the host

may or may not have symptoms, still infectious

• chronic infections

  • virus detected at all times

  • symptoms present or absent; may develop late

• latent infections

  • viral genome (provirus) remains silent in the host cell

  • infection is followed by a symptomless period (no virus detected), can reactivate

  • cannot be eliminated

categories distinguished by detection of virus during the period of persistence

• once somebody gets a cold sore the virus will be with them their whole life

• they stay in nerve cells potentially reactivating to cause cold sores later

viruses and human tumors

some cancers

• caused by oncogenic viruses

• result from integration of viral genome onto host DNA

  • cells transformed - viral genes are expressed

• uncontrolled growth results → tumors

other infectious agents - prions

proteinaceous infectious agents

reproduce by converting PrPc

• both normal PrPc and abnormal PrPsc proteins are present

  • sc for scrapie: one of the diseases it causes

• PrPsc interacts with PrPc

• PrPc is converted into PrPsc

• conversion continues and PrPsc accumulates

abnormal forms are bad bcuz they’re resistant to:

• proteases

• UV light

• standard autoclaving

transmitted by

• ingestion, transplant, and surgical instruments

causes fatal neurodegenerative diseases

• destroys brain tissue and develops sponge-like holes

• transmissible spongiform encephalopathies (TSEs)

  • animal disease

    • scrapie in sheep

    • mad cow disease in cattle

  • human disease

    • Kuru

    • Fatal familial insomnia

    • Creutzfeldt-Jakob disease

    • Variant Creutzfeldt-Jakob disease

symptoms may not appear for years after infection, always fatal

other infectious agents - viroids

short piece of ssRNA

• vary in size (246-375 nucleotides)

• all identified viroids infect plants and cause plant disease

  • examples:

    • potato spindle tuber

    • chrysanthemum stunt