2.4 Viral nucleic acids and genome types

Viral nucleic acids come in two flavors: DNA and RNA. These genetic blueprints dictate how viruses replicate and evolve. DNA viruses tend to be more stable, while RNA viruses mutate faster, leading to quick adaptations.

The Baltimore classification system groups viruses based on their genome type and replication strategy. This helps scientists understand how different viruses infect cells and make copies of themselves. Some viruses even split their genomes into segments, adding another layer of complexity.

DNA vs RNA Genomes

Structural Differences and Replication Sites

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• DNA viral genomes exist as single-stranded or double-stranded, linear or circular structures
• RNA viral genomes typically appear as single-stranded and linear molecules
• DNA viruses generally replicate within the host cell nucleus
• RNA viruses typically carry out replication in the cytoplasm
• DNA viruses often encode their own DNA polymerases for replication
• RNA viruses require RNA-dependent RNA polymerases or reverse transcriptases

Genome Stability and Mutation Rates

• DNA viral genetic material demonstrates higher stability
• DNA viruses exhibit lower mutation rates compared to RNA viruses
• RNA viral genomes show increased susceptibility to mutations
• Higher mutation rates in RNA viruses contribute to rapid evolution and adaptability
• DNA viruses generally possess larger genomes than RNA viruses (ranges from 3.2 kb for hepatitis B virus to 2400 kb for pandoraviruses)
• RNA virus genome sizes typically span from 3 kb (bacteriophage MS2) to 32 kb (coronaviruses)

RNA Genome Types and Integration

• RNA viral genomes classified as positive-sense, negative-sense, or ambisense
• Each RNA genome type necessitates distinct replication strategies
• Some DNA viruses can integrate their genomes into host cell DNA (human papillomavirus)
• Integration process rarely observed in RNA viruses, with exceptions (retroviruses)

Viral Genome Classification

Baltimore Classification System

• Categorizes viruses into seven classes based on nucleic acid type and replication strategy
• Class I: Double-stranded DNA genomes (herpesviruses, adenoviruses)
• Class II: Single-stranded DNA genomes (parvoviruses)
• Class III: Double-stranded RNA genomes (reoviruses)
• Class IV: Positive-sense single-stranded RNA genomes (picornaviruses, flaviviruses)
• Class V: Negative-sense single-stranded RNA genomes (orthomyxoviruses, rhabdoviruses)
• Class VI: Positive-sense single-stranded RNA viruses using reverse transcription (retroviruses)
• Class VII: Double-stranded DNA genomes using reverse transcription (hepadnaviruses)

Genome Structure and Replication Strategies

• Class I viruses utilize host cell DNA polymerases for genome replication
• Class IV viruses can immediately begin protein synthesis upon cell entry
• Class V viruses must first synthesize complementary positive-sense RNA before protein production
• Class VI and VII viruses require reverse transcription as part of their replication cycle
• Genome structure influences cellular localization of viral replication (nucleus for DNA viruses, cytoplasm for RNA viruses)
• Genome complexity often correlates with sophistication of replication strategies
• More complex genomes enable greater manipulation of host cell processes (poxviruses)

Genome Segmentation in Viruses

Characteristics and Distribution

• Genome segmentation involves division of viral genome into multiple discrete nucleic acid molecules
• More prevalent in RNA viruses, but also occurs in some DNA viruses
• Number of segments varies from two (arenaviruses) to twelve (some reoviruses)
• Each segment typically encodes one or more specific viral proteins
• Individual segments may possess their own regulatory elements
• Segmentation allows for genetic reassortment during co-infection (influenza viruses)
• Proper packaging of all segments into a single virion crucial for maintaining infectivity

Implications for Viral Evolution

• Genome segmentation contributes to viral evolution through genetic reassortment
• Reassortment can lead to emergence of new strains with altered virulence or host range
• Facilitates rapid adaptation to new environments or hosts
• Presents unique challenges in virus assembly and packaging
• Segmented genomes may offer advantages in gene regulation and expression
• Allows for modular evolution of viral components (influenza virus surface proteins)

Genome Type and Replication Strategies

DNA Virus Replication

• DNA viruses generally utilize host cell DNA polymerases for genome replication
• Replication typically occurs in the nucleus (exceptions include poxviruses)
• Some DNA viruses encode their own DNA polymerases (herpes simplex virus)
• DNA viruses often manipulate host cell cycle to optimize replication conditions
• Integration into host genome observed in some DNA viruses (human papillomavirus)

RNA Virus Replication

• RNA viruses require specialized viral enzymes for replication
• Positive-sense RNA viruses use their genome directly as mRNA for protein synthesis
• Negative-sense RNA viruses must first synthesize complementary positive-sense RNA
• Retroviruses employ reverse transcription to convert RNA genome into DNA
• RNA virus replication generally occurs in the cytoplasm (exceptions include influenza viruses)

Replication Fidelity and Evolution

• Error rates during replication higher in RNA viruses compared to DNA viruses
• Higher mutation rates in RNA viruses lead to more rapid evolution and adaptability
• DNA viruses exhibit greater genome stability and lower mutation frequencies
• Replication fidelity influences viral population diversity and adaptability to host defenses
• Some RNA viruses possess error-correction mechanisms to maintain genome integrity (coronaviruses)