Acellular and Prokaryotic Microbes

• Viruses

  • Smallest infectious agents (about 20nm – 300nm in diameter) and contain only one type of nucleic acid
  • Highly diverse organism, varying in size, shape, and genetic content
  • Very simple structures consisting essentially of a nucleic acid genome, protected by a shell of protein
  • May or may not have a lipoprotein envelope
  • Has no organelle
  • Metabolically inert and can only replicate inside a host cell
  • Genome consists of ONLY one type of nucleic acid; either RNA or DNA
  • Viral genome codes for the few proteins necessary for replication: some proteins are non-structural (e.g. polymerase, and some are structural, i.e. form part of the virion structure

  
• Virion

  Infectious virus particle
• Capsid


  • Protein shell which surrounds and protects the genome. It is built up of multiple (identical) protein sub-units called capsomers.
  • Capsids are either icosahedral or tubular in shape.

  
• Nucleocapsid


  Genome + capsid

  
• Envelope


  Lipoprotein membrane which surrounds some viruses, derived from the plasma membrane of the host cell

  
• Glycoproteins


  Proteins found in the envelope of the virion; usually glycosylated
• Classification of Viruses

  • Morphology
  • Chemical Composition and Mode of Replication
  • Classification of Viruses

  
• Morphology

  • Helical morphology is seen in many filamentous and pleomorphic viruses
  • Icosahedral morphology is characteristic of many "spherical" viruses
  • Icosahedral is a polyhedron having 20 faces
  • The number and arrangement of the capsomeres (morphologic subunits of the icosahedron) are useful in identification and classification
  • Many viruses also have an outer envelope

  
• Chemical Composition and Mode of Replication

  • The genome of a virus may consist of DNA or RNA, which may be single stranded (ss) or double stranded (ds), linear or circular
  • The entire genome may occupy either one nucleic acid molecule (monopartite genome) or several nucleic acid segments (multipartite genome)
  • monopartite genomes have a single molecule of nucleic acid
  • The different types of genome necessitate different replication strategies

  
• Classification of Viruses

  • dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
  • ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses)
  • dsRNA viruses (e.g. Reoviruses)
  • (+)ssRNA viruses (+ strand or sense) RNA (e.g. Picornaviruses, Togaviruses)
  • (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses)
  • ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses)
  • dsDNA-RT viruses (e.g. Hepadnaviruses)

  
• Origin of Viruses (Theories)

  • Coevolution Theory
  • Retrograde Evolution Theory
  • Escaped Gene Theory

  
• Viral Replication

  1. Attachment

  2. Penetration

  3. Uncoating

  4. Biosynthesis

  5. Assembly

  6. Release

  
• Attachment

  • Also known as adsorption
  • Highly specific
  • The surface of the virion contains structures that interact receptors on the surface of the host cell
  • It defines and limits the host species and type of cell that can be infected by a particular virus
  • Damage to the binding sites on the virion or blocking by specific antibodies (neutralization) can render virions non-infectious

  
• Penetration

  • The process whereby the virion enters the cell
  • As a result of fusion of the viral envelope with the plasma membrane of the cell or endocytosis

  
• Uncoating

  • The protein coat of the virion dissociates
  • The viral genome is released into the cytoplasm

  
• Biosynthesis

  1. Early Phase: Transcription of viral mRNA and translation of a number of non-structural proteins takes place

  2. Genome Replication: Multiple copies of the viral genome are synthesized by a viral polymerase

  3. Late Phase: Transcription and translation of viral mRNA and synthesis of the structural "late" proteins which are needed to make new virions

  
• Assembly

  1. The proteins self-assemble and a genome enters each new capsid

  2. This takes place either in the nucleus or in the cytoplasm of the cell, or sometimes, just beneath the cell surface

  
• Release

  1. Release of new infectious virions is the final stage of replication

  2. This may occur either by budding from plasma membrane (for enveloped viruses), or else by disintegration (lysis) of the infected cell (for non-enveloped viruses)

  3. Some viruses use the secretory pathway to exit the cell

  
• Pathogenic Mechanisms of Viral Disease

  • Implantation of virus at the portal of entry
  • Local replication
  • Spread to target organs (disease sites)
  • Spread to sites of shedding of virus into the environment

  
• Factors that Affect Pathogenic Mechanisms

  • Accessibility of virus to tissue
  • Cell susceptibility to virus multiplication
  • Virus susceptibility to host defenses
  • Natural selection favors the dominance of low-virulence virus strains

  
• Cellular Pathogenesis

  • Direct cell damage and death from viral infection may result from: Diversion of the cell's energy, Shutoff of cell macromolecular synthesis, Competition of viral mRNA for cellular ribosomes, Inhibition of the interferon defense mechanisms
  • Indirect cell damage can result from: Integration of the viral genome, Induction of mutations in the host genome, Inflammation, Host immune response

  
• Tissue Tropism

  • Cell receptors for virus
  • Cell transcription factors that recognize viral promoters and enhancer sequences
  • Ability of the cell to support virus replication
  • Physical barriers
  • Local temperature, pH, and oxygen tension enzymes and non-specific factors in body secretions
  • Digestive enzymes and bile in the gastrointestinal tract that may inactivate some viruses

  
• Implantation at the Portal of Entry

  • Virions implant onto living cells mainly via the respiratory, gastrointestinal, skin-penetrating, and genital routes (other routes can be used)
  • The final outcome of infection may be determined by the dose, location of the virus, infectivity and virulence

  
• Local Replication and Local Spread

  • Most viruses spread among cells extra-cellularly, but some may also spread intra-cellularly
  • Local infection may lead to localized disease and localized shedding of virus

  
• Dissemination from the Portal of Entry

  • Viremic: The most common route of systemic spread from the portal of entry is the circulation, which the virus reaches via the lymphatics
  • Neural: Dissemination via nerves usually occurs (e.g rabies, herpes and poliovirus)

  
• Congenital Infections

  • Infection of the fetus as a target "organ"
  • The virus must cross additional physical barriers
  • Transfer of the maternal defenses is partially blocked by the placenta, the developing first-trimester fetal organs are vulnerable to infection, and hormonal changes are taking place

  
• Antivirals

  • Prevent viral attachment and/or entry
  • Inhibit replication of the viral genome
  • Inhibit synthesis of specific viral protein(s)
  • Inhibit assembly or release of new infectious virions, or inactivate extracellular virus particles
  • Potential problem of the emergence of mutant virus strains resistant to a drug is always a concern

  
• Before Entry

  • Using agents which mimic the virus-associated protein (VAP) and bind to the cellular receptors
  • Using agents which mimic the cellular receptor and bind to the VAP
• Entry Inhibitor

  A number of "entry-inhibiting" or "entry-blocking" drugs are being developed to fight HIV

  
• Uncoating Inhibitor

  • Amantadine and rimantadine, have been introduced to combat influenza
  • These agents act on penetration/uncoating

  
• Reverse transcription

  By developing nucleotide or nucleoside analogues and deactivate the enzymes that synthesize the RNA
• Anti-viral agents

  Agents that can prevent:

  1. Viral attachment and/or entry

  2. Replication of the viral genome

  3. Synthesis of specific viral protein(s)

  4. Assembly or release of new infectious virions, or inactivate extracellular virus particles

  
• The potential problem of the emergence of mutant virus strains resistant to a drug is always a concern
• Before Entry

  Can be inhibited in two ways:

  a. Using agents which mimic the virus-associated protein (VAP) and bind to the cellular receptors

  b. Using agents which mimic the cellular receptor and bind to the VAP

  
• Uncoating Inhibitor

  Amantadine and rimantadine, have been introduced to combat influenza. They act on penetration/uncoating.

  
• Reverse transcription

  By developing nucleotide or nucleoside analogues and deactivate the enzymes that synthesize the RNA or DNA once the analogue is incorporated. This is associated with the inhibition of reverse transcriptase.
• Integrase

  Splices the synthesized DNA into the host cell genome

  
• Transcription

  Block attachment of transcription factors to viral DNA
• Translation


  Based on "antisense" molecules or ribozyme antivirals that have been developed to treat HIV infections

  
• Protease Inhibitors

  Used to treat selected patients with HIV infection