Viral Nucleic Acid and Types

Viral Nucleic Acid

• Viral genomes direct the production of proteins and nucleic acids within the host cell.
• DNA viruses utilize the host cell's replication machinery for replication.
• RNA viruses typically bring their own enzymes, such as RNA-dependent RNA polymerase, for replication.
• Viral nucleic acid is used to create viral mRNA, which is then translated into viral proteins by the host cell's ribosomes.
• The replication process differs based on whether the virus contains DNA or RNA.
• Some viruses, like HIV, integrate their genome into the host's genome.

Types of Viral Nucleic Acid

• Viruses are classified by their nucleic acid type.
• DNA viruses are further categorized into single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA).
• ssDNA viruses must be converted to dsDNA before replication.
• dsDNA is the most common type of DNA genome found in viruses.
• Most DNA viruses replicate their genome within the host cell nucleus using the host's DNA-dependent DNA polymerase for DNA synthesis and RNA polymerase for transcription.
• Some larger DNA viruses, like poxviruses, replicate in the cytoplasm using their own viral enzymes.
• RNA viruses primarily replicate in the host cell's cytoplasm.
• RNA viruses often use their own RNA-dependent RNA polymerase because host cells lack the necessary enzymes to replicate RNA from an RNA template.

Comparison of Viral Genome Types

• dsDNA: Herpesviruses, Adenoviruses - Stable genomes, rely on host DNA polymerase, can establish latent infections - Replication in the nucleus (mostly)
• ssDNA: Parvoviruses - Requires conversion to dsDNA before replication - Replication in the nucleus
• dsRNA: Rotavirus - Requires conversion to dsDNA before replication - Replication in the cytoplasm
• +ssRNA: Poliovirus, SARS-CoV 2 - RNA can act directly as mRNA - Replication in the cytoplasm
• -ssRNA: Influenza, rabies virus - Must package RNA polymerase for transcription of RNA - Replication in cytoplasm and nucleus
• ssRNA with DNA intermediate: HIV - RNA reverse transcribed into DNA, integrates into host genome - Replication in cytoplasm and nucleus
• Reverse transcribing DNA (dsDNA and RNA intermediate): Hepatitis B virus - DNA replicates via RNA - Replication in cytoplasm and nucleus

Capsid

• The capsid is a vital structural component of viruses, composed of protein subunits called capsomeres.
• The capsid protects the viral genome and helps in viral attachment to host cells.

Classification of Viruses

• Viruses can be classified based on:
  • The disease they cause (e.g., poliovirus, rabies virus)
  • The type of disease (e.g., murine leukemia virus)
  • Geographic location (e.g., Sendai virus, Coxsackie virus)
  • Their discoverers (e.g., Epstein-Barr virus)
  • How they were originally thought to be contracted (e.g., dengue virus, influenza virus)
  • Combinations of the above (e.g., Rous Sarcoma virus)

Classification of Viruses Based on Presence or Absence of Envelope

• Enveloped viruses have a lipid bilayer membrane surrounding their capsid, acquired from the host cell during budding.
  • They are sensitive to environmental conditions like heat, detergents, and desiccation due to the fragile lipid bilayer.
  • They often require close contact for transmission.
• Non-enveloped viruses lack this membrane.
  • They are more resistant to environmental factors.

The Baltimore Classification System

• This system categorizes viruses based on their genetic material and replication strategies into seven classes:
  • dsDNA viruses
  • ssDNA viruses
  • dsRNA viruses
  • (+) sense ssRNA viruses (codes directly for protein)
  • (-) sense ssRNA viruses
  • RNA reverse transcribing viruses
  • DNA reverse transcribing viruses

T-Even Phages

• T-phages are a specific class of bacteriophages, including T4 and T7, that infect E. coli.
• They have an icosahedral head, double-stranded DNA, and a tail with a sheath, base plate, and tail fibers.
• Their replication cycle involves:
  • Attachment to the bacterium
  • Insertion of genetic material
  • Replication
  • Lysis of the bacterium
  • Release of new viruses

Temperate Phages

• Lambda phages have an icosahedral head, a flexible non-contractile tail, and a single, double-stranded DNA molecule.
• They can integrate their genome into the host's genome, leading to lysogeny.

Filamentous Phages

• M13 is a filamentous bacteriophage with circular single-stranded DNA.
• It attaches to the F pilus of E. coli and does not kill the host.
• New viruses are released by budding.

Spherical Phages

• Bacteriophage phiX174 is an icosahedral phage that attaches to the host cell without a tail.
• It has a protein coat surrounding a core containing DNA and proteins.
• RNA phages include phages with RNA genomes, such as:
  • Human T-cell leukemia virus (HTLV)
  • Lentivirus group, including human immunodeficiency virus (HIV)

Orthomyxoviridae

• These are enveloped viruses with eight segments of linear, single-stranded, negative polarity RNA.
• They cause highly contagious airborne respiratory illnesses, with influenza virus being the primary human pathogen.

Paramyxoviridae

• Enveloped viruses with a helical nucleocapsid.
• Single-stranded, linear, nonsegmented, negative-polarity RNA.
• They include measles, mumps, parainfluenza, and respiratory syncytial viruses.

Rhabdoviridae

• Bullet-shaped enveloped viruses with a helical nucleocapsid.
• Single-stranded, linear, nonsegmented, negative-polarity RNA.
• They infect mammals, reptiles, fish, insects, and plants.
• Rhabdoviruses infecting mammals are grouped into two genera:
  • Vesiculovirus – containing vesicular stomatitis virus and related viruses like chadipura virus (arbovirus)
  • Lyssavirus – containing rabies virus and related viruses
• Rabies virus is a significant human pathogen.

Filoviridae

• Long threadlike viruses with a helical nucleocapsid.
• Single-stranded, linear, nonsegmented, negative-polarity RNA.
• Highly pleomorphic, long filaments.
• The two human pathogens are Ebola virus and Marburg virus, causing severe hemorrhagic fevers.

Coronaviridae

• Enveloped viruses with a helical nucleocapsid.
• Single-stranded, linear, nonsegmented, positive-polarity RNA.
• They have a prominent halo of spikes protruding from the envelope.
• Coronaviruses cause respiratory tract infections, such as the common cold, SARS, and COVID-19.
• Two genera found under this family:
  • Coronavirus
  • Torovirus