Biology pg. 250-266. Introduction to Virology

• The germ theory of disease demonstrated, by the late 1800s, that microscopic organisms such as bacteria are disease agents.
• Submicroscopic particles, not visible by light microscopy, can transmit certain diseases.
• Viruses were visualized and identified only after the electron microscope developed in the 1930s.
• Viruses, prions, and viroids have been identified as disease-causing agents since the development of the electron microscope.
• Viruses contain genetic material and undergo natural selection, similar to living organisms.
• Viruses cannot be considered cells or living organisms, as they do not conform to cell theory.
• Unlike cellular genomes, viral genomes are more diverse and may be composed of either DNA or RNA.
• Viruses are obligate intracellular parasites, which rely on host cell resources for viral activity because they cannot perform metabolism on their own.
• The basic features of viruses include viral structures and viral genomes.
• Red blood cells have a size of 10 μm.
• E. coli (bacterium) has a size of 3 μm.
• Bacteriophages have a size of 0.2 μm.
• HIV has a size of 0.15 μm.

Viral Structure

• A capsid, or protein coat, typically protects viral genetic material.
• Capsomeres, the protein subunits composing capsids, may have protein spikes attached.
• Capsids are usually made from identical capsomeres; however, certain viruses possess capsids composed of multiple distinct capsomere types.
• The primary determinant of viral morphology is the viral capsid.
• Some viral capsids are polyhedral, while others are helical, with a rod-like or filamentous shape
• Viruses range in size from 0.02 to 1 μm.
• A host is needed for reproduction.
• Some viruses have a phospholipid membrane from the host.
• Viruses do not have a nucleus.
• Viruses have a single- or double-stranded genome of DNA or RNA.
• Viruses do not have membrane-bound organelles.
• Viruses do not have ribosomes.
• Viruses do not have a cell wall.
• Viruses are not considered living.
• Complex viruses are those with more elaborate structures.
• The head of a bacteriophage has a polyhedral structure and contains genetic information.
• Capsids solely coat naked viruses.
• Enveloped viruses possess an additional viral envelope derived from the host cell's plasma membrane.
• A phospholipid bilayer with embedded proteins and glycoproteins makes up the viral envelope.
• The virus and/or the host organism can derive proteins that are embedded in the viral envelope.
• Proteins on the outer surface of viruses are responsible for its entry into the host cell, whether enveloped or naked.
• Although enveloped viruses contain a membrane derived from the host cell, this membrane is not considered a plasma membrane nor are enveloped viruses considered cells.

Viral Genomes

• Like cells, viruses contain nucleic acids.
• Unlike cellular organisms, viruses aren't restricted to using dsDNA.
• Viral genomes are relatively small with relatively few genes.
• Viral genomes can be composed of single- or double-stranded DNA or RNA.
• Viral genomes can be circular or linear.
• Viral genomes can be segmented, meaning they consist of more than one nucleic acid molecule.
• Viruses are classified by genome type because they lack typical cellular structures and metabolic pathways.
• All viruses must use host cells for translation.
• A virus can contain virally encoded DNA and RNA polymerase enzymes, which ensures they can express viral genes under varying conditions.
• RNA viruses must encode the necessary enzymes for replication and transcription because host enzymes use dsDNA templates for replication and transcription.
• Viral DNA is generally imported into the host nucleus upon infection with a dsDNA virus.
• Replication and transcription of viral genes occur similarly to the expression of host genes.
• Certain DNA viruses can carry out replication and transcription in the cytoplasm.
• ssDNA viruses use a ssDNA genome to synthesize a complementary DNA strand.
• Host or viral RNA polymerases are subsequently used to transcribe viral genes.
• ssDNA viruses must use the dsDNA template to synthesize a ssDNA copy of the genome before final virus assembly.
• RNA viruses that must use virally encoded RNA polymerase enzymes (RNA-dependent RNA polymerases) to transcribe viral RNA because Host RNA polymerase enzymes require a dsDNA template for transcription.
• ssRNA viruses can be classified as positive (+) or negative (-) sense.
• Positive (+) sense RNA is similar in sequence and directionality to host cell mRNA.
• Positive (+) sense RNA can be translated directly by host ribosomes without further modification.
• A positive (+) sense RNA is required by the host ribosome to synthesize the correct viral proteins for any type of RNA virus.
• Therefore, in the case of negative (-) sense RNA, before translation can take place, a complementary positive (+) sense copy must be synthesized using the (−) ssRNA strand as a template.
• To replicate a (+) ssRNA genome, a complementary (−) ssRNA strand must be created and used as a template to create more (+) ssRNA, which will be packaged into new virions.
• Replication of (-) ssRNA: Complementary (+) ssRNA is made for viral protein translation and to generate more copies of the (−) ssRNA genome for final viral assembly.
• dsRNA viruses are denatured upon entry into the host cell, and the (+) ssRNA strand can then be translated directly by host ribosomes to synthesize viral proteins.
• Each strand is used to make complementary (+) ssRNA and (-) ssRNA strands, which hybridize to create a complete dsRNA genome prior to final virus assembly.
• To make more dsDNA copies, host or viral DNA polymerase replicates both strands.
• To transcribe viral mRNA, host or viral RNA polymerase uses dsDNA as a template.
• To make more ssDNA copies, host or viral DNA polymerase synthesizes a complementary ssDNA strand to make dsDNA.
• To transcribe viral mRNA, complementary ssDNA strand is made and used by host or viral RNA polymerase.

(+) ssRNA

• Viral RNA polymerase synthesizes complementary (−) ssRNA strand to use as a template to make more (+) ssRNA copies.
• (+) ssRNA strand used directly during translation; (−) ssRNA can be used as a template by viral RNA polymerase to transcribe (+) ssRNA.

(-) ssRNA

• Viral RNA polymerase synthesizes complementary (+) ssRNA for use as a template to make more (−) ssRNA copies.

• Viral RNA polymerase uses (−) ssRNA strand as a template to transcribe (+) ssRNA for translation. dsRNA

• Viral RNA polymerase use (+) ssRNA strand as a template to make (−) ssRNA and vice versa. (+) ssRNA strand used directly during translation; (−) ssRNA can be used as a template by viral RNA polymerase to transcribe more (+) ssRNA copies.

Viral Life Cycles

• Viruses are metabolically inactive outside of a host cell as obligate intracellular parasites.
• The viral life cycle begins when a virus enters a host cell.
• In the host cell, the virus uses the host cell's resources and machinery to repilcate and release fully formed viral progeny (virions) to infect other host cells.
• A viral life cycle includes all activities from entry into a host cell to exit.
• The life cycles of bacterial and animal viruses and retroviruses are highlighted.

Bacteriophages

• Bacteriophages (or phages) are viruses which only infect bacteria.
• Bacteriophages typically have DNA genomes that are capsid coated.
• Unlike animal viruses, bacteriophages cannot become enveloped because of the rigidity of bacterial cell walls.
• Some bacteriophages have an elaborate capsid coating.
• Bacteriophages replicate through a lytic replication cycle.
  • Attachment: Phage tail fibers attach to the host bacterial cell surface.
  • Entry: The phage uses its tail sheath to inject the viral genome into the bacterial cytosol and the empty phage remains on the cell exterior.
  • Synthesis: Uses viral enzymes.
  • Assembly: Viral components like the head of the capsid, the tail sheath, and tail fibers are assembled, and viral genomes are packaged inside.
  • Release: Fully assembled virions are released, and the host cell lyses.
• Some bacteriophages can switch between a lytic replication cycle and a lysogenic replication cycle, in which bacteriophages can enter a latent phase for a variable period of time by incorporating viral DNA into a host chromosome to form a prophage.
• Expression of most viral genes is repressed, so the prophage doesn't stimulate either the synthesis or release of new virions.
• Prophage DNA is replicated with each new bacterial division (binary fission), and it remains latent within the bacterial population.
• Under certain conditions, the phage DNA is excised from the bacterial chromosome causing a lytic replication cycle to begin.
• Occasionally, a small piece of the bacterial chromosome is excised with the prophage DNA and transferred to the next host via transduction.

Animal Viruses

• Animal virus life cycles typically follow the same basic steps as the life cycles of bacteriophages; however, there are significant differences because of the fundamental differences between prokaryotic and eukaryotic cell biology.
• Animal viruses differ in the way in which they enter the host cell.
  • Direct penetration: Insertion of the viral genome into the host cell leaves an empty capsid on the host cell surface.
  • Endocytosis: The entire virion enters the cell intact.
  • Membrane fusion: The viral envelope and host plasma membrane fuse, and the capsid-coated virus enters the host cytoplasm.
• Viruses that enter the cell through membrane fusion or endocytosis must then be uncoated, which can occur in a phagolysosome or within the cytoplasm.
• Depending on the genome type, the viral genome may be imported into the host cell nucleus to initiate viral replication and gene expression, or the viral lifecycle can occur within the host cytosol.
• DNA replication and transcription may be mediated by host or virally encoded enzymes.
• Viral proteins may be synthesized either by cytosolic ribosomes or by ribosomes on the rough endoplasmic reticulum and traffc ked through the endomembrane system.
• Animal viruses can exit the cell via
  • Lysis: Naked virions exit the cell and result in host cell death.
  • Exocytosis: Both envelpoed and naked virions can exit, usually does not result in host cell death.
  • Budding: Enveloped viruses are released.
• During budding, the assembled virus travels to and pushes through the plasma membrane, creating a membrane coating around the virion. Viral glycoproteins (spikes) are trafficked to the host plasma membrane via the endomembrane system for viral attachment to the next host cell.

Retroviruses

• A subgroup of positive sense ssRNA animal viruses known convert linear ssRNA genomes into dsDNA.
• A unique viral life cycle requires reverse transcription of RNA to DNA, which is then put into the host chromosome.
• Upon viral entry and uncoating, retroviral (+) ssRNA is converted to dsDNA by a virally encoded enzyme called reverse transcriptase.
• The dsDNA copy is imported into the nucleus, and with the help of integrase, a virally encoded enzyme, viral DNA is integrated into a random region of the host cell's chromosome.
• Host RNA polymerase transcribes (+) ssRNA viral genome, which is packaged and then exits the cell via budding
• A virus that integrates into host cell DNA is called a provirus.
• Retroviruses resemble bacteriophage lysogeny.
• Descendants of the original infected host cell containing the provirus are also infected.
• Retrotransposons are a subclass of transposable elements thought to have originated from retroviruses because retrotransposons move through mRNA intermidiates using retroviral mechainsms. Sub viral Particles.

Sub-Viral Particles

• Viroids and prions have been discovered as nonliving infectious agents along with viruses.
• A viroid is a small, naked RNA molecule without a capsid and does not code for proteins.
• Prions are self-replicating proteins without any genetic material.

Viroids

• Viroids are subviral infectious particles, that consist of a short, circular ssRNA molecule that has no protein capsid
• They have regions of self-complementarity, resulting in ds regions within.
• Viroid replication is thought to occur via host RNA polymerases.
• These can bind host RNA sequences via complementary base pairing, resulting in host gene silencing.
• Most known viroids infect plants; however, hepatitis D virus resembles viroids and is a virus capable of infecting and causing disease in humans.

Prions

• A misfolded version of a cell surface protein known as PrPC is called a prion (PrPSc).
• Prions can cause the misfolding of additional wild-type PrP proteins.
• Prions do not contain any genetic material like organisms, viruses, and viroids do.
• Prion diseases are often neurodegenerative because wild-type PrP proteins are highly expressed in the cells of the central nervous system.
• Conversion to a prion form can occur by the spontaneous conversion of the wild-type PrP protein structure.
• Prion diseases can result from genetic mutations, so are therefore heritable).
• An infectious CJD form may be acquired via consumption of products from cattle that have BSE, otherwise known as mad cow disease.
• Prions act as infectious by causing changes to the secondary structure of other wild-type PrP proteins to produce more prions.
• Post-translationally, structural changes to wild-type PrP proteins occur and involve the refolding of a-helices to form B-pleated sheets.
• By inducing wild-type PrP proteins to change conformation, prions increase the number of prion proteins; therefore, they replicate and don't require initiating new gene expression.
• Newly formed prions aggregate and form amyloid fibrils because misfolded prion proteins are less soluble than wild-type PrP proteins.
• Once prion aggregation reaches a critical threshold, cellular functions are disrupted and result in disease.