🦠Virology Unit 10 – Viral Life Cycle: Entry to Assembly

Key Concepts

• Viruses are obligate intracellular parasites that require host cells for replication
• Viral life cycle consists of several stages: entry, uncoating, replication, assembly, and release
• Viruses can have DNA or RNA genomes, which can be single-stranded or double-stranded, linear or circular
• Viral genomes can be segmented (influenza) or non-segmented (measles)
• Viruses encode structural proteins that form the capsid and envelope, as well as non-structural proteins involved in replication and host cell interactions
• Viral tropism refers to the specificity of a virus for a particular host cell type or tissue
• Viral pathogenesis is determined by factors such as route of entry, replication efficiency, and host immune response

Viral Entry Mechanisms

• Viruses attach to specific receptors on the host cell surface using viral attachment proteins (hemagglutinin in influenza)
• Receptor binding can induce conformational changes in the viral proteins, facilitating entry
• Viruses can enter cells via direct fusion with the plasma membrane (HIV) or through endocytosis followed by fusion with endosomal membranes (influenza)
  • Direct fusion occurs when the viral envelope fuses directly with the host cell membrane, releasing the viral genome into the cytoplasm
  • Endocytosis involves the internalization of the virus in a membrane-bound vesicle, which then fuses with endosomal membranes to release the viral genome
• Some viruses (adenovirus) enter cells through receptor-mediated endocytosis and escape from endosomes using viral proteins that disrupt the endosomal membrane
• Viral entry can be pH-dependent (influenza) or pH-independent (HIV), depending on the specific fusion mechanism
• Antibodies targeting viral attachment proteins can neutralize the virus and prevent entry (neutralizing antibodies)

Uncoating and Genome Release

• After entry, the viral capsid is disassembled in a process called uncoating, which releases the viral genome into the host cell cytoplasm or nucleus
• Uncoating can be triggered by changes in pH (influenza), interactions with host cell factors, or viral proteases that degrade the capsid
• The site of uncoating depends on the virus; some uncoat in the cytoplasm (picornaviruses), while others uncoat in the nucleus (herpesviruses)
• Viral genomes can be released as naked nucleic acids (poliovirus) or as nucleoprotein complexes (influenza)
  • Naked nucleic acids are immediately accessible for translation or replication
  • Nucleoprotein complexes require further processing to release the genome
• Viral proteins may facilitate the transport of the genome to the appropriate cellular compartment for replication (nuclear localization signals)

Viral Replication Strategies

• Viral replication strategies depend on the nature of the viral genome (DNA or RNA, single-stranded or double-stranded)
• DNA viruses typically replicate in the nucleus using host cell machinery and viral DNA-dependent DNA polymerases (herpesviruses)
  • Some DNA viruses (poxviruses) replicate in the cytoplasm using viral enzymes
• RNA viruses replicate in the cytoplasm using viral RNA-dependent RNA polymerases (RdRps)
  • Positive-sense RNA viruses (poliovirus) can directly translate their genome into proteins, which then replicate the genome
  • Negative-sense RNA viruses (influenza) must first transcribe their genome into positive-sense mRNA using viral RdRps
• Retroviruses (HIV) use a unique replication strategy involving reverse transcription of the RNA genome into DNA, which is then integrated into the host cell genome
• Viral replication often involves the formation of replication complexes, which concentrate viral and host factors needed for efficient replication
• Viral replication can be error-prone, leading to high mutation rates and the generation of viral quasispecies

Protein Synthesis and Processing

• Viral proteins are synthesized using the host cell translation machinery, including ribosomes and tRNAs
• Viral mRNAs can be monocistronic (encoding a single protein) or polycistronic (encoding multiple proteins)
  • Polycistronic mRNAs are translated using strategies such as internal ribosome entry sites (IRES) or ribosomal frameshifting
• Viral proteins can be synthesized as polyproteins, which are then cleaved into individual proteins by viral or host proteases (picornaviruses)
• Post-translational modifications, such as glycosylation and phosphorylation, can be important for viral protein function and stability
• Viral proteins can be targeted to specific cellular compartments using signal sequences or through interactions with host cell proteins
• Viral proteins can have multiple functions, such as acting as structural components of the virion and as enzymes involved in replication

Viral Assembly

• Viral assembly involves the packaging of the viral genome and proteins into new virions
• Assembly can occur in the cytoplasm (picornaviruses), nucleus (herpesviruses), or at the plasma membrane (influenza)
• Viral structural proteins self-assemble to form the capsid or nucleocapsid
  • Capsid assembly can be guided by scaffolding proteins, which are later removed
• Enveloped viruses acquire their lipid envelope by budding through host cell membranes (plasma membrane or intracellular membranes)
  • Viral envelope proteins are inserted into the host cell membrane and interact with the capsid or matrix proteins to drive budding
• Viral genomes are packaged into the capsid through specific interactions between the genome and viral packaging signals or proteins
• Maturation of the virion can involve conformational changes in the capsid proteins or cleavage of precursor proteins by viral proteases (HIV)

Host Cell Interactions

• Viruses interact with host cell factors at every stage of the viral life cycle
• Viral proteins can manipulate host cell signaling pathways to create a favorable environment for replication (suppression of innate immune responses)
• Viruses can induce host cell shutoff, where host cell protein synthesis is inhibited to prioritize viral protein synthesis (influenza)
• Viral infection can lead to cytopathic effects, such as cell lysis or apoptosis, which can contribute to disease pathogenesis
• Host cell restriction factors can inhibit viral replication at various stages (APOBEC3G inhibits HIV replication)
  • Viruses have evolved mechanisms to counteract or evade host cell restriction factors (HIV Vif protein degrades APOBEC3G)
• Viral proteins can interact with host cell proteins to facilitate viral replication or spread (HIV Tat protein recruits host factors to enhance transcription)

Clinical and Research Applications

• Understanding the viral life cycle is crucial for the development of antiviral drugs and vaccines
• Antiviral drugs can target specific stages of the viral life cycle, such as entry (maraviroc for HIV), replication (acyclovir for herpesviruses), or protein processing (protease inhibitors for HIV)
• Vaccines can be designed to elicit neutralizing antibodies that prevent viral entry or cell-mediated immune responses that target infected cells
  • Live attenuated vaccines (measles) contain weakened viruses that can replicate but not cause disease
  • Inactivated vaccines (polio) contain killed viruses that cannot replicate but still elicit an immune response
• Viral vectors, such as adenoviruses or lentiviruses, can be used to deliver genes of interest for gene therapy or vaccine development
• Studying viral replication and host cell interactions can provide insights into fundamental cellular processes and the discovery of new host factors
• Viral diagnostics rely on detecting specific stages of the viral life cycle, such as the presence of viral antigens (rapid influenza tests) or viral nucleic acids (PCR for SARS-CoV-2)