3.1 DNA and RNA viral genomes

Viral genomes come in two flavors: DNA and RNA. Each type has unique features that affect how viruses replicate, evolve, and interact with their hosts. Understanding these differences is key to grasping viral behavior and developing strategies to combat them.

DNA viruses tend to have larger, more stable genomes that replicate in the nucleus. RNA viruses, on the other hand, have smaller, more mutation-prone genomes that usually replicate in the cytoplasm. These distinctions shape viral life cycles and impact how they evade host defenses.

DNA vs RNA Genomes

Molecular Composition and Structure

Top images from around the web for Molecular Composition and Structure

• 

  DNA and RNA ‹ OpenCurriculum View original

  Is this image relevant?

• 

  Structure and Function of RNA | Microbiology View original

  Is this image relevant?

• 

  Introduction to Nucleic Acids | Biology for Non-Majors I View original

  Is this image relevant?

• 

  DNA and RNA ‹ OpenCurriculum View original

  Is this image relevant?

• 

  Structure and Function of RNA | Microbiology View original

  Is this image relevant?

1 of 3

Top images from around the web for Molecular Composition and Structure

• 

  DNA and RNA ‹ OpenCurriculum View original

  Is this image relevant?

• 

  Structure and Function of RNA | Microbiology View original

  Is this image relevant?

• 

  Introduction to Nucleic Acids | Biology for Non-Majors I View original

  Is this image relevant?

• 

  DNA and RNA ‹ OpenCurriculum View original

  Is this image relevant?

• 

  Structure and Function of RNA | Microbiology View original

  Is this image relevant?

1 of 3

• DNA viral genomes consist of deoxyribonucleic acid while RNA viral genomes contain ribonucleic acid resulting in fundamental differences in their chemical structure and properties
• DNA viral genomes can be single-stranded or double-stranded, linear or circular while RNA viral genomes are typically single-stranded but can also be double-stranded in some cases (rotaviruses)
• The sugar component in DNA viral genomes involves deoxyribose whereas RNA viral genomes contain ribose affecting the overall stability and flexibility of the genetic material
• DNA viral genomes utilize thymine as one of the four nucleotide bases while RNA viral genomes replace thymine with uracil
• Molecular weight and size of DNA viral genomes are generally larger than RNA viral genomes with some exceptions (mimivirus)
  • DNA genomes range from a few thousand base pairs to over a million base pairs
  • RNA genomes typically range from a few thousand to tens of thousands of bases

Genome Organization and Complexity

• DNA viruses like herpesviruses have complex genomes with multiple genes and regulatory elements while RNA viruses often have more compact genomes with overlapping reading frames
• RNA viral genomes can be positive-sense, negative-sense, or ambisense each requiring different replication strategies
  • Positive-sense RNA genomes act as mRNA (hepatitis C virus)
  • Negative-sense RNA genomes require complementary RNA synthesis (influenza virus)
  • Ambisense RNA genomes contain both positive and negative-sense regions (arenaviruses)
• Many RNA viral genomes possess unique structures facilitating translation and replication
  • Cap analogs mimic host mRNA 5' caps (flaviviruses)
  • Internal ribosome entry sites (IRES) allow cap-independent translation (picornaviruses)
  • Genome-linked proteins (VPg) act as primers for RNA synthesis (poliovirus)
• Some DNA and RNA viral genomes exhibit segmentation where genetic material divides into multiple distinct molecules
  • Influenza viruses (RNA) have 8 segments
  • Some bacteriophages (DNA) have segmented genomes (φ6 phage)
• Certain DNA and RNA viral genomes contain repetitive sequences or inverted terminal repeats playing crucial roles in replication and packaging
  • Adenoviruses (DNA) have inverted terminal repeats for replication initiation
  • Bunyaviruses (RNA) have complementary terminal sequences for genome circularization

Implications of Genome Type

Replication Strategies and Cellular Localization

• DNA viruses typically replicate in the host cell nucleus utilizing host cell machinery for transcription while most RNA viruses replicate in the cytoplasm using virus-encoded RNA-dependent RNA polymerases
• Genome type influences the viral replication cycle
  • DNA viruses often follow a DNA-to-RNA-to-protein pathway (herpes simplex virus)
  • RNA viruses may directly produce proteins from genomic RNA (picornaviruses) or require an intermediate step (retroviruses)
• RNA viral genomes particularly those of retroviruses can integrate into the host genome through reverse transcription potentially leading to long-term persistence and altered host gene expression (HIV)

Host Interactions and Immune Responses

• Genome type affects virus susceptibility to host antiviral responses with RNA viruses often triggering different innate immune pathways compared to DNA viruses
  • RNA viruses activate RIG-I-like receptors (RLRs) (influenza virus)
  • DNA viruses stimulate cyclic GMP-AMP synthase (cGAS) (herpes simplex virus)
• Complexity and size of viral genomes influence their ability to encode proteins modulating host cell processes and immune responses
  • Larger DNA viruses generally have more diverse arsenals of immunomodulatory proteins (poxviruses)
  • RNA viruses often encode multifunctional proteins to maximize coding capacity (flaviviruses)
• Genome type impacts virus ability to undergo recombination and reassortment which are important mechanisms for viral evolution and emergence of new strains
  • Influenza viruses (RNA) undergo frequent reassortment leading to antigenic shift
  • Coronaviruses (RNA) exhibit high rates of recombination contributing to cross-species transmission

Stability and Mutation Rates

Genome Stability and Mutation Frequency

• DNA viral genomes are generally more stable than RNA viral genomes due to inherent chemical stability of DNA and presence of proofreading mechanisms in many DNA polymerases
• RNA viral genomes have higher mutation rates typically $10^{-3}$ to $10^{-5}$ mutations per nucleotide per replication cycle compared to DNA viral genomes with rates around $10^{-8}$ to $10^{-11}$ mutations per nucleotide per replication cycle
• Higher mutation rates of RNA viruses contribute to their rapid evolution and ability to escape host immune responses but also increase likelihood of deleterious mutations
• DNA viruses often employ host cell DNA repair mechanisms to maintain genome integrity while RNA viruses lack access to these systems contributing to their higher mutation rates
  • Mismatch repair corrects DNA replication errors in herpesviruses
  • Base excision repair removes damaged bases in poxviruses

Factors Influencing Mutation Rates

• Error-prone nature of RNA-dependent RNA polymerases which lack proofreading activity serves as a major factor in high mutation rates observed in RNA viruses
• Concept of quasispecies a cloud of closely related viral variants appears more pronounced in RNA virus populations due to their higher mutation rates affecting their adaptability and pathogenesis
  • HIV exists as a diverse population of variants within a single host
  • Hepatitis C virus quasispecies contribute to treatment resistance
• Stability differences between DNA and RNA viral genomes influence their persistence in the environment and ability to maintain infectivity outside of host cells
  • DNA viruses like smallpox can remain infectious in scabs for extended periods
  • RNA viruses such as influenza are generally less stable outside the host