Virus Structure and Capsid Functions

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Virus Structure

• A virion is a complete, infectious viral particle.
• A capsid is a protein coat surrounding the nucleic acid, composed of protein subunits (capsomeres).
• The nucleocapsid (core) is the nucleic acid enclosed by the capsid.
• Envelopes are made of lipids and proteins (host-derived) and may contain glycoproteins (spikes) for host receptor recognition.
• Most animal viruses are enveloped, while most bacterial and plant viruses are naked.

Functions of the Capsid

• The capsid protects the viral genome, packaging the nucleic acid.
• Non-enveloped viruses deliver genomes through direct penetration (genome alone enters the cell) or endocytosis (whole virus engulfed and capsid uncoated).
• For enveloped viruses, the membrane fuses with the host cell membrane, releasing the capsid into the cell cytoplasm.

Capsid Morphology

• Helical viruses have hollow, cylindrical capsids.
• Icosahedral viruses have many-sided capsids.
• Complex viruses have complicated structures.

Helical Capsid Viruses

• Helical capsids have spiral or rod shapes.
• Length is determined by the nucleic acid length, and the width by the capsomere size and packaging.
• Helical capsids typically contain single-stranded RNA (ssRNA).

Icosahedral Capsid Viruses

• Icosahedral capsids are spherical and rigid.
• They enclose the nucleic acid inside an identical triangular faces and vertices.
• They are efficient and use the fewest capsomeres for assembly.
• Many animal viruses have icosahedral capsids (e.g., adenovirus, poliovirus, HPV).

Complex Viruses

• Complex viruses don't have a simple icosahedral or helical symmetry.
• Bacteriophages are complex, including a polyhedral capsid and a helical tail sheath.
• Poxviruses are brick-shaped.

Enveloped Virions

• Enveloped virions are acquired via budding from the host cell, during viral replication.
• Envelope proteins, as well as glycoproteins often play significant roles in host recognition.
• Envelopes protect viruses from the immune system.
• Enveloped viruses are more fragile than naked viruses.

Delivery of Genome from Enveloped Virions

• Enveloped virions enter host cells via endocytosis (engulfing the virus into the host cell) or membrane fusion (viral envelope and host membrane fuse).
• Uncoating of the capsid releases the genome.

DNA and RNA Viruses

• Viruses can be enveloped or non-enveloped, irrespective of their nucleic acid type (DNA or RNA).
• There's no correlation between virus genome structure and its envelope status.

Virus Particles (Virions)

• Virions are metastable, meaning they're stable during protection of the genome, but become unstable during infection, leading to structural changes for genome release.
• Viral metastability is achieved via symmetrical arrangement of identical proteins for maximal contact.

RNA Viruses

• RNA viruses encode or carry RNA-dependent RNA polymerase (RdRP) for replication, as mammalian cells lack this enzyme.

Viral Genomes

• Viral genomes can be DNA or RNA, single-stranded or double-stranded.
• Some genomes are linear, others circular or segmented.
• Viral genomes typically contain a limited number of genes (4 to hundreds).

(+) vs. (-) Sense RNA and DNA

• mRNA (ribosome ready) is always the positive (+) strand.
• RNA and DNA complements of (+) strands are the negative (-) strands.
• Negative-sense RNA must be converted to (+) sense RNA before translation.

Eukaryotic DNA and RNA Viruses

• Eukaryotic DNA viruses typically replicate in the nucleus, or cytoplasm (e.g. poxviruses).
• Eukaryotic RNA viruses usually replicate in the cytoplasm.

RNA Viruses Challenge Central Dogma

• RNA viruses carry or encode the enzymes necessary for replication and transcription (RNA-dependent RNA polymerase).
• Retroviruses are an exception to this because they use reverse transcription (RNA to DNA).

Polymerases

• DNA polymerases synthesize DNA using DNA templates (DNA-dependent DNA polymerase). RNA templates can sometimes be used (RNA-dependent DNA polymerase).
• RNA polymerases synthesize RNA using DNA templates (DNA-dependent RNA polymerase). RNA templates can sometimes be used (RNA-dependent RNA polymerase).

Genome Replication and Expression of RNA Viruses

• RNA viruses replicate their genomes and synthesize viral mRNAs usually via an RNA-dependent RNA polymerase.
• Exceptions include retroviruses.

Viral Classification

• Viruses are classified based on various attributes (e.g., nucleic acid type, symmetry, presence/absence of an envelope, host range).
• The International Committee on Taxonomy of Viruses (ICTV) provides a standardized classification system.
• The Baltimore classification system is based on genome composition, replication, and mRNA production, for better understanding of DNA/RNA virus groups.