13 Viruses, Viroids, and Prions

agents

Viruses, Viroids and Prions are collectively called [__]

→ not organisms/living → acellular: not composed of cells

→ lacks metabolic processes

Requires hosts in order to replicate themselves

Viroid

Infectious RNA.

Short piece of ssRNA (single-stranded RNA) that varies in size, 246-375 nucleotides

All identified [__]s infect plants and cause plant diseases

eg.

• potato spindle tuber → elongates potato’s and doesn’t make them as meaty

• Chrysanthemum stunt → causes flowers to not be as big as they’d normally be

Prion

Infectious protein, i.e,

Proteinaceous infectious agents that are misfolded proteins. Also referred to as PrP^SC (prion protein scrapie, in reference to scrapies in sheep where it was first found)

• reproduces by ability to interact with and cause misfoldings in PrP^c (prion protein, cellular), or normal proteins in our neurons

resistant to:

• Proteases: enzymes that break down proteins

• UV light

• Standard autoclaving

transmitted by:

• ingestion of contaminated food

• transplantation

• surgical instruments

transmissible spongiform encephalopathies

Prions causes fatal neurodegenerative diseases in their accumulation in neural tissue

→ brain tissue develops sponge-like holes

→ sponge-like appearance led to name of [__] (TSEs) » refers to all prion diseases

eg. in Animals

• Scrapie in sheep

• Mad cow disease in cattle

in Humans

• Kuru → occurred due to cannibalism

• Fatal familial insomnia → runs in families, as genotypes have proteins that are more likely to convert to abnormal form. Symptoms is being unable to sleep till death

• Creutzfeldt-Jakob disease → occurs in older people. The missionary had this when Aborgines ate them, leading to Kuru

• Variant Creutzfeldt-Jakob disease→ occurred from eating contaminated beef (mad cow disease)

Virion

Complete, infectious virus particle. Consists of only a nucleic acid and protein coat.

Obligate Intracellular Parasite

Viruses are [__], meaning they can only reproduce within their host cells

• uses host machinery to replicate

• inactive outside of host

• eg. bacteriophage: a virus that infects bacteria

capsid

Viral structure. The protein coat of a virus. Surrounds the nucleic acid

» nucleic acid could only be either RNA or DNA (not both)

» together with the nucleic acid it surrounds, it becomes the nucleo[__]

Envelope

Viral structure. Refers to the outer lipid bilayer, outside of the capsid, that some viruses have.

» naked viruses: viruses that lack an [__]

→ exit infected cells by lysing

» enveloped viruses: viruses that have a [__]

→ exit infected cells by budding

Spikes

Viral structure. Refers to the structures on the surface of a virus that help bind (adhere) to host cell receptors. It’s these structures that cause an immunological response by the host.

Icosahedral

1/3 of the shapes of a virus

Appears spherical when viewed with an electron microscope, but are actually 20 flat triangles arranged in a shape of a soccer ball

helical

2/3 of the shapes of a virus

Appear cylindrical when viewed with an electron microscope. Actually have their capsomeres arranged in a helix, similar to spiral staircase

Complex

3/3 of the shapes of a virus

More complicated structures.

eg. Phages

» an icosahedral nucleocapsid head

» long helical protein tail that has other components attached to it

100

Viruses are notably small

• 10-[__]x smaller than bacteria

• smallest is ~10nm (~10 genes)

• largest is ~800nm

host range

Number of different hosts that a virus can infect. Usually limited to a single species for a single virus (as viruses can infect all life forms)

Further limited by:

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

• restriction-modification system in host cell → restriction enzymes cut up viral DNA to make sure host cell isn’t infected → something that a virus must overcome in order to infect

suitable

Viruses only multiply inside a [__] living cell, and thereby must face specific techniques and conditions in the lab to ensure their growth

plaque method

Method of growing bacteriophages in bacterial cells for lab

• bacteriophages form plaques: clearings of agar from the bacteriophage causing bacterial lysing

• each plaque rose from a single phage → plaque-forming units (PFU)

  • a single PFU represents a single infectious phage that successfully targeted and replicated in a host cell and lysed it

embryonated

Animal viruses are grown in

• living animals (mice, rabbits, pigs)

• [__] eggs → how flu vaccine is developed

  • influenza vaccine made in duck eggs

Tissue

[__] culture or cell culture grow human cells → used as host cell for viruses that can only infect humans

Lytic Cycle

½ Replication cycles undergone by bacteriophages to reproduce → this cycle is not exclusive to bacteriophages however

• phages multiply inside a cell

• phage lyses cell to release virions

5 step process:

1. attachment (adsorption as it removes virus from solution when attached to host cell)

2. penetration → DNA/RNA get injected in host cell

3. synthesis

→ Nucleic replication

→ Transcriptions/translation

4. assembly (maturation) done in a sequential manner

5. release

» has a burst size (number of viruses produced per bacterial cells) of T4 phage is 200 virions

Lysogenic cycle

2/2 Replication cycles undergone by bacteriophages to reproduce → exclusive for bacteriophages

• phage integrates its genome into the host genome

• phage released without killing the host cell

Specifically undergone when replicating a temperate virus: a virus that can infect a host cell but does not immediately kill it (contrary to viral viruses)

→ can undergo both lytic and [__]s at different times

Steps:

1. Attachment

2. Penetration

3. Incorporation of viral DNA into host chromosome

» reverse transcriptase → turns viral RNA into DNA (cDNA)

» integrase: enzyme that inserts viral DNA into host genome

» prophage: what the virus is called (provirus in eukaryotes) when integrated into (doesn’t destroy) the host DNA

4. Viral DNA is replicated when the host cell replicates

5. Prophage can excise out (as it needs to be outside of the genome to replicate) and undergo lytic cycle

Lysogenic state

When phages do not outright kill their host cell and remains integrated in their DNA (to replicate alongside with), it is said to have entered the [__] or Lysogenic cycle.

Superinfection

1/3 effects of viral infection on host cells

Host cells are immune to [__]: infection by the same phage.

» builds up immunity

transduction

2/3 effects of viral infection on host cells

Horizontal transfer of bacterial genes

Recall: when bacterial DNA is accidentally packaged into one phage (by drifting into the phage) and transferred that way » can pack any gene

Standard [__]

Lysogenic conversion

3/3 effects of viral infection on host cells

i.e, Phage conversion » the conferring of new properties to cell as a result of a bacterial DNA being packaged into all phages replicated due to an excision error » only DNA adjacent to the integrated phage can be transferred

Specialized transduction.

diagnostic tests

Diagnosing viral infections are determined more by a patient’s symptoms rather than using actual tests

If utilizing tests, such [__] include:

• culturing the virus

• detecting virus by

  • molecular techniques (PCR) → most common

  • electron microscope

  • serology → injected into animals to see what antibody they’ll produce; takes antibodies to test it against different viruses and see which one it’d react with

transmission

Animal diseases are classified based on their route of [__]

Enteric Virus

Animal virus transmitted via fecal-oral route

• causes gastroenteritis » inflammation of the lining of the stomach and intestines; some cause systemic disease

eg. norovirus, rotavirus

Respiratory viruses

Animal virus transmitted via infected respiratory droplets

• Generally, remain localized in respiratory tract

eg. SARS-Cov-2, influenza

Zoonotic virus

Animal virus transmitted from animal to human (cross species barrier)

eg. rabies, HIV, SARs-Cov-2 as well

Sexually transmitted viruses

Animal virus transmitted by sexual activities

• can cause lesions on genitalia only or systemic infections

eg. HIV, herpes, simplex virus

uncoating

Animal virus replication has 5 steps:

1. Attachment » done through specific spikes that adhere to receptors of host cell

→ (why only one virus can affect specific species, w/ exceptions like influenza)

2. Entry and [__]: fusion or endocytosis

→ enveloped viruses can do both, while unenveloped can only fuse

→ capsid discarded simultaneously with entry of virion in host cell, or if it’s nearing the synthesis site

2. Synthesis → nucleic acid synthesized in nucleus, while proteins in cytoplasm

3. Assembly » encapsidation: packaging nucleic acid into capsid occurs at nucleus → nucleocapsid

4. Release

→ budding: virus gets its envelope from host cell » how enveloped viruses are released

→ lysing cell » how non-enveloped viruses are released; released when the host cell dies (via virion programmed apoptosis)

defense

The outcome of infection of eukaryotic cells depends on host [__]

• acute infection: rapid onset, usually short in duration, more severe.

• persistent infection: continue for years or a lifetime. viruses are always present in the host

• some viruses exhibit both (eg. HIV)

Acute infection

Infection that is rapid on onset but usually short in duration and more severe

• Large number of viruses gets produced

• disease symptoms usually due to tissue damage (cell death)

• host develops immunity (either short or long lasting)

Persistent infection

Infection that continue for years or a lifetime

• viruses are always present in the host

• may or may not have symptoms, but still infectious regardless

Chronic infections » virus is detected at all times

Latent infections » viral genome becomes provirus (injects itself in our genome); remains silent in the host cell.

Can be distinguished by their detection during period of persistence

eg. Chicken pox and cold sores

Chronic infection

Persistent infection. Virus is detected at all times. Symptoms present or absent; may develop late

Latent infection

Persistent infection. Viral genome (provirus) remains silent in the host cell. Infection is followed by a symptom-less period and can reactivate. cannot be eliminated

oncogenic

Some cancers are caused by

• [__], or tumor-forming, viruses

• integration of viral genome onto host DNA → cell transformation and viral genes expressed (lysogenic conversion)

• expressed properties are uncontrolled growth → tumors