Virology Notes

Coronavirus

  • Envelope
  • Genetic material and nucleocapsid
  • E-Protein
  • Spikes
  • Spike glycoprotein (S)
  • M-Protein

Bacteriophage

  • Genetic material
  • Capsid head
  • Sheath proteins
  • Tail fibers

Chapter 17: Viruses

  • Examples of viruses:
    • Bacteriophage (DNA)
    • Tobacco mosaic virus (RNA)
    • Adenovirus (DNA)
    • Influenza virus (RNA)

Viruses

  • A submicroscopic infectious agent that replicates only inside the living cells of an organism (Virions).
  • Associated with a number of plant, animal, and human diseases.
  • Found in every ecosystem on Earth.
  • Most numerous type of “biological entity".

History of Virology

  • French chemist Louis Pasteur suggested that something smaller than a bacterium was the cause of rabies.
  • Pasteur used the word “virus,” Latin for poison.
  • Dmitri Ivanovsky (1892, Russian) and Martinus Beijerinck (1898, Dutch) are credited as co-discovering viruses.
  • They found that there were extremely minuscule infectious agents.
  • Both scientists first noticed the infectious agent while working with Tobacco Mosaic Virus.

Virus Characteristics

  • Can only reproduce using the metabolic machinery of the host cell.
  • Noncellular.
  • May have a DNA or RNA genome.
  • The invention of the electron microscope allowed these infectious agents to be seen for the first time.
  • French chemist Louis Pasteur suggested that something smaller than a bacterium was the cause of rabies.
  • Louis supported this with a filtration experiment using a porcelain filter.
  • Pasteur used the word “virus,” Latin for poison.

Are Viruses Alive?

  • Characteristics of Life:
    • Organized
    • Requires material and energy (have a metabolism)
    • Maintain homeostasis and respond to the environment
    • Reproduce and develop
    • Have adaptations

Why Viruses Are Not Considered Alive

  • Organized: They have organization, but are not made of cells.
  • Requires material and energy (have a metabolism): They use the host’s cell to carry out these processes.
  • Maintain homeostasis and respond to the environment: They can’t keep themselves in a steady state, though they have some response to the environment.
  • Reproduce and develop: They use the host’s cell to replicate, but don’t grow/develop; not capable of independent replication.
  • Have adaptations

Viral Diseases in Humans

  • Sexually transmitted diseases: AIDS (HIV), genital warts, genital herpes, Zika
  • Childhood diseases: Mumps, measles, chickenpox, German measles
  • Respiratory diseases: Common cold, influenza, severe acute respiratory syndrome (SARS)
  • Skin diseases: Warts, fever blisters, shingles
  • Digestive tract diseases: Gastroenteritis, diarrhea
  • Nervous system diseases: Poliomyelitis, rabies, encephalitis, Zika
  • Other diseases: Smallpox, Zika, cancer, hepatitis, mononucleosis, yellow fever, dengue fever, conjunctivitis, hepatitis C, Ebola

Structure of Viruses

  • Each type has at least two parts (capsid and core).
  • Viruses are characterized by:
    • Size and shape (10 to 400nm400 nm in diameter)
    • Type of nucleic acid core (single-stranded or double-stranded? DNA or RNA?)
    • Capsid or no capsid (outer layer composed of protein subunits): can be icosahedral or helical
    • Some are enveloped by membrane
    • Others are “naked”

Virus Structure Components

  • Covering:
    • Capsid (protein)
    • Envelope (not found in all viruses)
  • Inner core:
    • Nucleic acid molecule (DNA or RNA)
    • Various proteins (enzymes)
  • Non-enveloped virus (Adenovirus):
    • Capsid (protein shell)
    • Genome
  • Enveloped virus (lentivirus):
    • Envelope
    • Genome
    • Capsid (protein shell)

Examples of Viruses

  • Adenovirus: DNA virus with a polyhedral capsid and a fiber at each corner.
  • T-even bacteriophage: DNA virus with a polyhedral head and a helical tail.

Parasitic Nature of Viruses

  • Viruses are obligate intracellular parasites.
  • Cannot reproduce outside a living cell.
  • Are either active or inactive, instead of living or non-living
  • Can be cultured only inside living cells, such as:
    • Chicken egg
    • Tissue culture

Viruses: Host Specificity

  • Viruses are host-specific, meaning that viruses are capable of reproducing in the cells of a specific organism.
  • Host specificity is determined by the structure of molecules on the capsid or the spikes on an enveloped virus.
  • Attach in a lock-and-key manner with a susceptible receptor on the host cells outer surface and gain entry.
  • Anything without the receptor will not allow entry; cell will not be infected.
  • Many antiviral medications interfere with the attachment of viruses to host cells by interfering with that lock-and-key system.

Viral Origin and Evolution

  • Viruses do not fossilize, so understanding their evolution is difficult.
  • Proteins and nucleic acids (organic molecules in viruses) evolved, and viruses may have arisen from these two basic polymers when cells did, but it is not known how.
  • Three hypotheses about viral origin and evolution:
    • Viruses may have been derived from pieces of cell genomes.
    • Viruses may have evolved backwards from living cells.
    • Viruses degenerated from living cells.

Reproduction of Animal Viruses

  • Animal virus enters the host cell.
  • Uncoating releases viral DNA or RNA.
  • Budding:
    • Viral particles are released in a bud.
    • Acquires a membranous envelope.

Viral Classification

  • Viruses are non-living and hard to classify.
  • The International Committee on Taxonomy of Viruses (ICTV) came up with a classification system that differs from how we classify living organisms.
  • Includes only taxonomic levels of order – family, genus, species.
  • Does not include higher orders (domain, kingdom, phylum, and class).
  • Over 2,500 species of viruses have been identified.
  • When new viruses emerge within one species of virus, additional classification types are added (Ex. Influenza A or SARS-CoV-2).
  • May be named based on proteins that are present on the envelope (ex. flu viruses H1N1, named for the hemagglutinin [H] and neuraminidase [N] spikes).

Types of Viruses

  • Can be classified based on the type of nucleic acid present (RNA, DNA, or both at different stages of the life cycle).
  • Can be single-stranded (ss) or double-stranded (ds).
  • The majority of viruses have RNA genomes.
  • Can also be classified based on the type of transmission (Ex. retroviruses, like HIV, have proteins that cause reverse transcription in the host cell).

Flu Virus

  • A flu virus has an H (hemagglutinin) spike and an N (neuraminidase) spike. Eg Influenza virus
  • H spike allows the virus to bind to the receptor.
    • 16 different types
  • N spike attacks host plasma membranes.
    • Allows mature viruses to exit the cell
    • 9 different types
  • Each type of spike can occur in different varieties.
  • Our immune system only recognizes H spikes and N spikes it has been exposed to.
  • Currently, the H7N9 and H5N1 subtypes of the flu virus are of great concern because they can potentially become pandemics (global outbreaks).

Spikes of a Seasonal Flu and Bird Flu

  • Mutation and reassortment can lead to new combinations of spikes on human influenza viruses.

Emerging Viruses

  • Emerging viruses are new or previously uncommon illnesses.
  • Examples are coronavirus (COVID), Zika, Middle East respiratory syndrome (MERS), AIDS, West Nile encephalitis, Ebola hemorrhagic fever, and avian influenza (bird flu).

Events Causing Emergence of Viruses

  • Several types of events can cause the emergence of viruses:
    • A virus may extend its range (e.g., West Nile was transported to the US and took hold in birds and mosquitoes).
    • A genetic mutation may occur (e.g., Influenza strains H5N1, H1N1, and H7N9 were created through the mutation of flu viruses which only infected animals).
  • It is necessary to obtain a flu vaccine each year due to the rapidly mutating flu virus.

Viruses, Viroids, and Prions

  • Viruses are best known for causing infectious diseases in plants and animals (e.g., Herpes, HIV, some cancers).
  • Viruses lack metabolism; thus, antibiotics have no effect.

Viroids

  • Naked strands of RNA
  • Many are crop diseases

Prions

  • Protein molecules with a contagious tertiary structure
  • Misfolded protein that can induce misfolding of normal variants of the same protein and trigger cell death
  • Prions cause prion diseases called transmissible spongiform encephalopathies (TSEs).
  • TSEs are neurodegenerative diseases which destroy nerve tissue in the brain.
  • They are untreatable and fatal.

Prion Diseases (TSEs)

  • TSEs are neurodegenerative diseases which destroy nerve tissue in the brain.
  • They are untreatable and fatal.
  • Some human and other animal diseases:
    • Mad cow disease
    • Scrapies (sheep and goats)
    • Chronic wasting disease (deer)
    • Creutzfeldt-Jakob disease (human)
  • Transmission can occur through:
    • Consumption of infected brains
    • Defective protein transmitted via contaminated harvested human brain products (corneal grafts, dural grafts, etc.)
    • Some cases can be familial
    • Kuru – very rare disease resulting from funerary cannibalism, formerly common among the Fore people of Papua New Guinea

Chronic Wasting Disease (CWD)

  • Spreading in the US since the mid-2010s.
  • Disease may manifest 18-24 months after initial exposure.
  • Potential for transmission to humans.
  • As a precaution, hunters should avoid eating deer and elk tissues known to harbor the CWD agent (e.g., brain, spinal cord, eyes, spleen, tonsils, lymph nodes) from areas where CWD has been identified.