Virology: Viral Entry, Replication, and Life Cycle

Why We Need Viruses

• Elimination of of all viruses would likely result death in about 2 days
• Most viruses are not pathogenic to humans
• Viruses help with ecosystems, fungi, plants, etc.
• Bacteriophages (viruses that infect bacteria) keep bacteria from taking over
• By killing bacteria in the oceans, viruses allow Plankton to survive and produce oxygen
• Oncolytic viruses are a type of virus

Properties of a Virus

• Viruses are filterable agents and obligate intracellular parasites
• Viruses cannot make energy or proteins independently of a host cell
• Viral genomes may be RNA or DNA, but not both
• Viruses have a naked capsid or an envelope morphology
• Viral components are assembled and do not replicate by "division"

Consequences of viral properties

• Viruses must be able to use the host cell processes to produce their components (viral messenger RNA, protein, and identical copies of the genome).
• Viruses must encode any required processes not provided by the cell.
• Viral components must self-assemble.

Viral Structure

• Knowledge of a virus's structural (size and morphology) and genetic (type and structure of nucleic acid) features provides insight into how the virus replicates, spreads, and causes disease.
• Structures of a naked icosahedral capsid virus and enveloped viruses with an icosahedral nucleocapsid or a helical ribonucleocapsid
• Helical nucleocapsids are always enveloped for human viruses

Capsid Morphology and the Envelope

• Viral nucleic acid is surrounded by a capsid (single- or double-layer protein shell)
• Nucleic acid + capsid = nucleocapsid
• Icosahedral contains 20 triangular faces & 12 vertices subunits (soccer ball shape)
• Helical has varied subunits, a spherical core tight with specific viral capsid proteins
• Viral envelope is a membrane made of lipids, proteins, and glycoproteins
• A Nonenveloped particle is relatively stable & resistant to temp. changes, acids, proteases, detergents, & drying
• An Enveloped viruses is more fragile & susceptible to heat, acids, detergents & drying, therefore it MUST STAY WET & are generally transmitted in fluids
• Virus-specific envelope glycoproteins protrude from the outer surface of the envelope
• i.e. SARS-CoV-2 spike protein

Classifying Viruses

• Classification of viruses is done according to:
• Structure: size, morphology, and nucleic acid (e.g., picornavirus [small RNA], togavirus)
• Biochemical characteristics: structure and mode of replication
• This is the current means of taxonomic classification of viruses.
• Disease: encephalitis and hepatitis viruses, for example
• Means of transmission: arbovirus spread by insects, for example
• Host cell (host range): animal (human, mouse, bird), plant, bacteria
• Tissue or organ (tropism): adenovirus and enterovirus, for example
• Retroviruses were discovered before knew it caused SPECIFIC disease, therefore they called it an Orphan virus

Glycoproteins

• Most viral glycoproteins have asparagine-linked (N-linked) carbohydrates
• Glycoproteins extend through the envelope and away from the surface of the virion
• Spike glycoproteins are major antigens that elicit protective immunity
• Some glycoproteins act as VAPs (Virus Associated Pyramids) that are capable of binding to structures on target cells
• If they (VAPs) bind erythrocytes = hemagglutinins (HAs)
• Other glycoproteins include neuraminidase (NA; influenza), Fc receptor & C3b receptor (HSV)
• Naked viruses can also express certain glycoproteins, even if they aren't bound to envelop, just the capsid (i.e. adenoviruses)

Main Groups of Human Viruses

• Includes RNA and Dna viruses
• Includes linear and circular viruses
• Includes enveloped and non-enveloped viruses

Test Your knowledge

• What are the main shapes of a virus?
• Icosahedral and Helical

The Six Stages of Establishment of Infectious Diseases and Outcomes

• Encounter
• Entry
• Spread
• Multiplication
• Damage
• Outcome

Encounter and Entry

• There are Four Main Routes of Encounter and Entry:
• Respiratory
• Gastrointestinal
• Transcutaneous
• Sexual
• Viruses can either be Exogenous or Endogenous
• Most viral diseases come from exo.
• Endo= reactivation of latent virus from within host cell, e.g. HSV,VZV (shingles)

Spread and Multiplication

• Vertical versus horizontal spread describes how the virus spreads amongst people
• Vertical = fetus infected in-utero
• Horizontal = virus spreads between members of susceptible host population
• Physiological spread:
• Neural = virus spreads through nerves, i.e. HSV, rabies, VZV
• Hematogenous = carried in the blood, i.e. CMV, HIV, EBV, high titer in bloodstream=viremia
• Some viruses have multiple pathways for spread, i.e. VSV skin & neural
• Incubation Period = the period between exposure to an infection and the appearance of the first symptoms

Damage during infection

• Signs & symptoms of viral disease are the culmination of a series of interactions between virus & host

Intrinsic and Extrinsic Mechanisms

• Intrinsic Protective Mechanisms:
• Apoptosis
• Autophagy ("self" "eating")- cellular stress response viral sequestration & degradation in cytoplasmic organelles called autophagosomes
• Extrinsic Protective Mechanisms:
• Barriers
• Innate immune responses-
• Toll like receptors (TLRs)- pattern recognition receptors that identify conserved patterns in pathogens
• Interferon- inhibit virus replication indirectly by inducing the expression of cellular proteins that inhibit the protein synthesis machinery
• Cell-mediated immunity- NK cells (innate), Cytotoxic T-cells (adaptive)
• Adaptive immune response
• Neutralizing antibodies destroy infectivity of virus
• Antibody-dependent cell-mediated cytotoxicity- antibodies lyse infected cells

Three Types of Viral Infections

• *Acute infection- virus undergoes multiple rounds of replication, results in death of host cell or host successfully controls virus
• *Chronic infection- virus particles continue to shed after acute illness, sometimes without host death; host doesn't successfully control virus. Usually RNA viruses
• *Latent infection- does not result in production of progeny viruses; host may or may not have "controlled" virus.
• DNA viruses or retroviruses. Can Reactivate. Can cause cellular transformation -> cancer
• What is the best way to prevent viral infection?
• Getting Vaccinated!
• Washing hands, covering coughs, staying home when sick

Viral Life Cycle

• Attachment, Entry, Uncoating, Synthesis of protein & nucleic acid, Assembly, Release

Attachment, Entry and Uncoating Details

• Attachment occurs when A virus attaches to host cell adhesion receptors on the surface Enveloped viruses use surface spike proteins which contains One or more attachment proteins
• Naked viruses: surface-exposed capsid regions mediate attachment Tissue tropism is when viruses Bind to specific receptor(s)
• Entry occurs after the Virion moves along host cell surface where it encounters entry receptors
• During Entry, Membrane fusion means the virus Fuses with host membrane & nucleocapsid is released
• Endocytosis can occur, and the virus is uncoated inside cell
• Uncoating is where virions disassembled and capsid is removed to make viral genome accessible to the cellular transcription & translation machinery

Viral Synthesis: Protein & Nucleic Acid

• Viral protein synthesis depends on if a virus single or double stranded and whether it's DNA or RNA
• This will be relevant later when learning about different viruses

Viral Nucleic Acid and Sense

• Viral Nucleic acid comprises the viral genome
• DNA viruses move to the nucleus for genome replication (poxviruses are an exception)
• Immediate-early and early transcription produces the enzymes and proteins needed for late transcription Early transcription is followed by genome replication and late transcription produces the capsid structural proteins
• Assembly results in the formation of the nucleocapsid
• Most RNA viruses replicate in the cytoplasm (exceptions include influenza and retroviruses). Most are single-stranded.
• The RNA virus genome encodes RNA-dependent RNA polymerases as well as the enzymes necessary for viral mRNA processing.
• Self-assembly of the genome and structural proteins produces the nucleocapsid.
• Viruses are classified according to the Polarity of their strand of RNA
• Positive-sense strand viral genomes act as mRNA for protein synthesis, so translation can begin immediately. Naked positive-sense viral genomes are infectious.
• Negative-sense strand viral genomes do not immediately begin transcription. They Act as template for synthesis of a positive-sense strand, which is then used for protein synthesis. Naked negative-sense strand viral genomes are not infectious by themselves.
• Be aware that there are exceptions and complications to this classification system

Viral Genetics

• Recombination is where genetic information is exchanged between viruses or a virus and its host
• Reassortment is where viruses w/ segmented genomes create hybrid strain, this can cause antigenic shift
• Complementation occurs if gene products or functions of a mutated virus is "complemented" by another virus.
• Phenotypic mixing is where the genome is not from the same virus as its protein coat.

Release by Viruses

• Nonenveloped release usually only happens when the cell lyses
• Lytic virus = burst out of host cell killing it
• Lysogenic virus = integrate into host genome and replicates within the genome until triggered
• Exocytosis = reverse phagocytosis
• Enveloped: budding out of host cell, Some cause apoptosis, some are non-lethal
• M-protein: inner surface of envelope & touches nucleocapsid
• Stabilizes glycoprotein & lipid envelope interaction and Direct viral genome to sites of virus assembly so the cell can help Virus budding

Explore viral entry mechanisms in naked and enveloped viruses. Understand replication inhibitors like amantadine and enfuvirtide. Learn about antigenic shift, HDV's replication strategy, and the characteristics of viral life cycles.