Virology: Overview

Viruses are infectious, obligate intracellular parasites composed of a nucleic acid core surrounded by a protein capsid. Viruses can be either naked (non-enveloped) or enveloped. The classification of viruses is complex and based on many factors, including type and structure of the nucleoid and capsid, the presence of an envelope, the replication cycle, and the host range. The replication cycle differs between viruses that infect bacteria (bacteriophages) and viruses that infect eukaryotic cells. Bacteriophages have either a lytic or lysogenic replication cycle, while eukaryotic viruses have a defined 6-step replication process.

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Viruses are infectious, obligate intracellular parasites, composed of a nucleic acid core (deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) surrounded by a protein capsid; at times, viruses are also surrounded by an envelope derived from host cell membranes.

Types of viruses

Variety of viruses in existence, including size and morphology

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Basic structure consists of: 

  • Inner “machinery” that allows the virus to replicate within host cells 
  • Outer structural component that allows the virus to survive in the environment and bind to host cells
Anatomy of a virus

Anatomy of a virus

Image: “Anatomy of a virus” by DEXi. License: CC0.

Inner components

  • Viral genome (nucleoid): diverse, composed of either RNA or DNA
  • Viral enzymes: required for viral replication within the host cell:
    • DNA-dependent RNA polymerase
    • RNA-dependent RNA polymerase
    • RNA-dependent DNA polymerase (reverse transcriptase)

Outer components

  • Capsid:
    • Single- or double-layer protein shell that surrounds the nucleoid
    • Arranged of subunits, known as capsomers
    • 3 structural patterns:
      • Icosahedral
      • Helical
      • Complex
  • Envelope:
    • May or not be present
    • Surrounds nucleocapsid
    • Composed of virus-specific proteins, lipids, and carbohydrates (derived from host cell membranes)
Viral capsids shapes

Viral capsids can have a (a) helical, (b) polyhedral, or (c) complex shape.

Image: “Figure 6.6”, access for free at License: CC BY 4.0.


Rna viruses flowchart classification

RNA virus identification:
Viruses can be classified in many ways. Most viruses, however, will have a genome formed by either DNA or RNA. RNA genome viruses can be further characterized by either a single- or double-stranded RNA. “Enveloped” viruses are covered by a thin coat of cell membrane (usually taken from the host cell). If the coat is absent, the viruses are called “naked” viruses. Viruses with single-stranded genomes are “positive-sense” viruses if the genome is directly employed as messenger RNA (mRNA), which is translated into proteins. “Negative-sense,” single-stranded viruses employ RNA dependent RNA polymerase, a viral enzyme, to transcribe their genome into messenger RNA.

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Multiple categorization schemes exist for viruses, based on physical characteristics and replication strategies.

Table: Classifications of viruses
Classification by: Types
Type and structure of nucleoid
  • DNA or RNA:
    • For RNA viruses:
      • Single-stranded (ss-RNA) genome (positive or negative sense)
      • Double-stranded (ds-RNA) genome
    • For DNA viruses: All are ds-DNA (except for Parvoviridae).
  • Linear or circular
  • Segmented or non-segmented
Structure of capsid
  • Icosahedral
  • Helical
  • Complex symmetry
Presence of envelope
  • Naked
  • Enveloped
Replication cycle (for bacteriophages)
  • Lytic
  • Lysogenic or temperate
  • Host range
  • Immunologic characteristics
  • Sensitivity toward certain chemicals or physical properties


It is important to differentiate between the replication of bacteriophages (viruses that infect bacteria) and eukaryotic viruses (viruses that infect eukaryotic cells).

Replication cycle of bacteriophages

There are 2 pathways of replication once a virus is within the bacterial host cell:

  1. Lytic cycle:
    • Occurs under conditions of DNA damage or other stresses
    • Bacteriophage takes over host cell transcription and translation machinery (immediate and rapid phage gene and protein expression).
    • Causes lysis of bacterial host cell 
  2. Lysogenic or temperate cycle:
    • Bacteriophage genomes incorporated in bacterial host genome
    • Phage genome is then replicated in a benign, dormant state: The phage genome may be expressed when the bacteria cell is stressed (e.g., nutrient depletion).

Replication cycle of eukaryotic viruses

  • Viral genome released in infected host cell
  • Steps of viral replication:
    1. Attachment: Specialized viral proteins attach to host cell.
    2. Penetration: invasion of host cell
    3. Uncoating: capsid dismantled and genetic material made available
    4. Biosynthesis: viral nucleic acid and proteins synthesized
    5. Assembly: virions assembled within the host cell
    6. Release: via host cell lysis (for naked viruses) or the budding of the cell membrane (for enveloped viruses)
  • All DNA viruses replicate in the nucleus (except for the poxvirus).
  • All RNA viruses replicate in the cytoplasm (except for influenza and retroviruses).

Genetic Diversification

Viruses have evolved many processes to increase their genetic diversity:

  • Recombination: exchange of genes between 2 chromosomes by crossover at homologous regions
  • Reassortment:
    • Viruses with segmented genomes exchange genetic material.
    • May cause an antigenic shift (e.g., influenza virus)
  • Complementation:
    • Occurs when the virus has a mutation that results in a non-functional protein
    • A non-mutated virus “complements” a mutated virus (when co-infected in a host cell) by making a functional protein that serves both viruses (e.g., the hepatitis D virus (HDV) requires the hepatitis B virus (HBV) to supply HBsAg (a key envelope protein for HDV)).
  • Phenotypic mixing:
    • Simultaneous infection of host cell with 2 viruses
    • Usually involves the mixing of the genome of 1 virus with surface proteins of the 2nd virus
Viruses genetic diversification

Viruses have evolved diverse strategies for increasing genetic diversity including recombination (the exchange of genes between 2 chromosomes by crossover at homologous regions), reassortment (exchange of segments of chromosomes), complementation (the exchange of genetic material from a functional virus with a nonfunctional virus to convert the latter into functional) and phenotypic mixing (mixing of 2 viral genomes a simultaneously infected host cell giving rise to progeny with blended genomes).

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Special Cases


  • RNA viruses 
  • Contain reverse transcriptase (RNA-dependent DNA polymerase)
  • Most prominent retrovirus is the human immunodeficiency virus (HIV).


  • Not technically viruses
  • Infectious proteins that do not contain a nucleoid
  • Cause transmissible spongiform encephalopathies:
    • Creutzfeldt-Jakob disease 
    • Kuru
    • Bovine spongiform encephalopathy (“mad cow” disease)


  1. Baron, S. (1996). Medical microbiology. University of Texas Medical Branch at Galveston.
  2. Parker, N., Schneegurt, M., Thi Tu, A.H., Lister, P., & Forster, B. Microbiology. (2016). Chapter 6.2, The Viral Life Cycle.

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