Viral Molecular Biology: Structure, Replication, Entry, and Pathogenesis

Viral Structure and Classification

Capsid and Nucleocapsid

The capsid is the protein shell that protects the viral nucleic acid genome from nucleases. The nucleocapsid consists of the capsid and the genome together. Viruses can be classified as naked viruses (without an envelope) or enveloped viruses (with a lipid membrane surrounding the capsid).

• Capsid protein: Encodes structural proteins for the virus.

• Viral receptor-binding protein: Facilitates attachment to host cells.

• Genome composition: Can be single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), or DNA.

Genome and Viral Dependency

Viruses are dependent on host cells for replication, as they lack the necessary machinery for independent reproduction. Genome length and composition vary greatly among viruses, including large "giruses."

Viral Replication Cycle

Attachment

Viruses attach to host cells via specific proteins on their surface that bind to corresponding receptor molecules on the host cell membrane. This lock-and-key interaction determines host specificity.

• Example: HIV binds to CD4 receptors on T-helper cells; rhinoviruses bind to ICAM-1 receptors on respiratory cells.

Entry (Penetration)

Viruses enter host cells through several mechanisms:

• Membrane Fusion: Enveloped viruses fuse their membrane with the host cell membrane, releasing the viral core into the cytoplasm.

• Endocytosis: Viruses are engulfed by the host cell, forming a vesicle that transports the virus inside.

• Genetic Injection: Bacteriophages inject their genetic material into the host cell, leaving the capsid outside.

Uncoating

After entry, the virus sheds its protein coat (capsid) to release its genetic material into the host cell. Uncoating is often triggered by the low pH of vesicles inside the cell.

Replication and Biosynthesis

Viruses hijack the host's cellular machinery to produce new viral components. This includes:

• Viral protein production: Synthesis of enzymes and structural proteins.

• Genome replication: DNA viruses replicate in the nucleus; most RNA viruses replicate in the cytoplasm.

Assembly (Maturation)

New viral proteins and genomes are assembled into immature virus particles. This process can occur in the nucleus or cytoplasm, depending on the virus.

Release (Egress)

New viruses exit the host cell by:

• Lysis: Host cell bursts, releasing viruses and killing the cell.

• Budding: Enveloped viruses acquire their membrane by budding from the host cell, allowing continued virus production.

Molecular Hurdles of the Host Cell

Barriers to Viral Infection

Eukaryotic cells present several barriers to viral infection:

• Receptors and polymerases: Host RNA-dependent RNA polymerases cannot replicate viral genomes; viruses encode their own polymerases.

• Actin remodeling: Affects all stages of viral replication.

• Ribosome and mRNA compatibility: Host machinery translates monocistronic RNAs; viruses use alternative splicing, segmented genomes, or polyproteins.

• Virus–host mRNA competition: Viruses produce abundant proteins to outcompete host gene expression.

Genetic Diversity in RNA Viruses

RNA viruses mutate rapidly due to the lack of proofreading ability in RNA polymerases, leading to high genetic diversity.

Targets for Antiviral Therapies

• Drugs must target essential viral processes and be non-toxic to the host.

Mechanisms of Viral Entry and Spread in the Body

Preferred Routes of Entry

Viruses enter hosts through skin or mucous membranes:

• Respiratory tract

• Gastrointestinal tract

• Genital tract

• Conjunctiva

• Crossing the placenta

Respiratory Tract Entry

The most frequent route, as inhaled droplets introduce viruses into the lungs. Examples include rhinoviruses, coronaviruses, and influenza viruses.

Gastrointestinal Tract Entry

Viruses enter via the faecal-oral pathway, requiring resistance to stomach acid and digestive fluids.

Genital Tract Entry

Viruses enter through abrasions or infect cells in the reproductive tract, often associated with sexually transmitted infections.

Conjunctiva Entry

The conjunctiva is a thin, transparent tissue covering the eye. Viruses can cause diseases such as epidemic keratoconjunctivitis, conjunctivitis, and uveitis.

Other Routes of Entry

• Skin: Requires a breach for viral entry.

• Bone marrow or organ transplants

• Transfusion and blood products

• Iatrogenic induction

Mechanisms of Viral Spread and Pathogenesis

Routes of Transmission

Viruses are transmitted between hosts via:

• Respiratory droplets

• Gastrointestinal (faecal-oral) route

• Skin breaches

• Genital tract (sexual contact)

• Vertical transmission: Mother to child (transplacental, intrapartum, postnatal)

Viral Infections and Pregnancy

Viruses can cross the placenta, causing severe outcomes such as spontaneous abortion, stillbirth, neonatal death, or congenital malformations (teratogenic effects).

Spread Within the Host

• Local spread: Virus spreads to neighboring cells, either extracellularly or via cell fusion.

• Systemic spread: Hematogenous spread (via bloodstream) and neurotropic spread (via nerves).

Virus Exit: Shedding

Shedding and Zoonosis

Viruses are usually shed from their routes of entry. Zoonotic viruses (spread from animals to humans) are emerging pathogens, often with segmented genomes (e.g., hantaviruses, arenaviruses, SARS, MERS, rabies, Ebola).

Survival of Viruses in the Environment

Factors Affecting Survival

• Virus composition

• Presence in human/animal wastes

• Temperature, humidity, pH

Human Viruses in Water Environments

Humans are exposed to enteric viruses through contaminated shellfish, crops irrigated with wastewater, and polluted recreational/drinking water. Viruses are more stable in water than bacteria.

Groundwater Safety

Groundwater is a source for many wells. Outbreaks, such as norovirus in Wisconsin (2007), highlight the risk of viral contamination.

Patterns of Disease

Types of Viral Infection

• Acute infection

• Acute infection followed by persistent latent infection

• Chronic infection with continuous shedding

• Slow infection

Additional info:

• Viruses alter host cell metabolism by redirecting resources to viral replication, often suppressing host gene expression.

• Viral factories (replication compartments) are specialized regions in the host cell where viral replication is concentrated, increasing efficiency and protecting viral components from host defenses.

• DNA viruses and RNA viruses differ in their replication sites and mechanisms: DNA viruses typically replicate in the nucleus, while RNA viruses replicate in the cytoplasm and often require virus-specific polymerases.