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VIRAL LIFE CYCLE © A viral life cycle is the series of steps a virus undergoes to infect a host cell, replicate its genome, produce viral proteins, assemble new virions, and exit the cell. © Understanding the viral life cycle is essential for: 1. Developing antiviral drugs that target specific stages of replication. 2. Vaccine design by identifying viral proteins critical for immunity. 3. Predicting disease outcomes based on tissue tropism and host range. 4. Controlling viral transmission in populations Overview of the viral life cycle: C The life cycle generally follows a common sequence of stages Attachment (Adsorption) Entry (Penetration) and uncoating Genome Replication Protein Expression ak WN Virion assembly and release STEP 1: ATTACHMENT OF VIRUS TO HOST CELL > Viral Attachment (Adsorption) Viral attachment is the initial step in viral infection. 0 © The virus binds to specific receptors on the host cell surface. © The viral surface proteins involved are either capsid or envelope glycoproteins. © The surface protein recognize and bind to specific host cell receptors. P . Viral Attachment (Adsorption) Key features of viral attachment. oO 1. Specificity. * Virus recognize and bind to specific host cell receptors. * This interaction host range and tissue that it can infect. 2. Viruses often require one or more receptors (Receptors and Co-receptors) to attach effectively. P . Viral Attachment (Adsorption) Key features of viral attachment. oO 3. Attachment process involves a five-step process. A. Viral Attachment (Adsorption) C Three Factors influencing viral attachment. 3. Environmental Factors: * This include physical or chemical conditions surrounding the virus and host cell that affect binding such as a) Temperature: Extreme temperatures can alter viral protein structure or receptor availability. b) pH: Certain viruses require specific pH levels for optimal binding or to trigger conformational changes in viral proteins. c) Ionic conditions: Salt concentrations and ions can influence protein folding and receptor-virus interactions * Example: Influenza virus HA requires endosomal acidification (low pH) to trigger fusion after attachment. A. Viral Attachment (Adsorption) © Biological significance of viral attachment. 1. Determines host specificity and tissue tropism. * Hepatitis B virus infects hepatocytes due to expression of the NTCP receptor. * Influenza virus preferentially infects respiratory epithelial cells expressing sialic acid residues 2. Major target for antiviral strategies: 3. Neutralizing antibodies can block receptor binding. 4. Entry inhibitors prevent conformational changes or receptor engagement. A. Viral Attachment (Adsorption) C Biological significance of viral attachment. 3. Influences viral pathogenesis and spread i.e. * Infectivity: How easily the virus establishes infection. * Spread within the host determining which tissues are infected. * Transmission: Ability to infect new hosts. STEP 2: VIRAL ENTRY AND UNCOATING B. Viral Entry (Penetration) and Uncoating © A virus must enter the cell and release its genome before replication can begin. © This process occur after a virus is attached to a host cell. W These steps vary depending on virus structure (enveloped vs. non-enveloped) and host cell characteristics, W These involves two critical process; 1. Entry (Penetration) - gaining access into the host cell cytoplasm. 2. Uncoating - releasing the viral genome so replication can begin. B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration) © Viral entry is the process by which the virus crosses the host plasma membrane. © Viral entry occur via three major pathways; 1. Membrane fusion (for enveloped viruses) 2. Receptor-mediated endocytosis (most Common Pathway). 3. Direct penetration (only non-enveloped viruses) B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration): © Viral entry occur via three major pathways; 1. Membrane Fusion (For Enveloped Viruses) *% Key steps in membrane fusion: a) Attachment triggers conformational change in fusion proteins b) Fusion peptides insert into the host membrane. c) Lipid bilayers merge. d) Capsid enters the cytoplasm and beings uncoating. B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration): © Viral entry occur via three major pathways; 1. Membrane Fusion (For Enveloped Viruses) * Biological significance of membrane fusion: a) Allows rapid viral entry without need for endocytosis. b) Occurs at the cell surface (unlike endocytosis-dependent viruses). c) Important for viruses infecting cells with low endocytic activity (e.g., T cells for HIV). B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration): © Viral entry occur via three major pathways; 2. Receptor-Mediated Endocytosis * It is the most common pathway for both enveloped and non-enveloped viruses. * Key steps in membrane fusion: a) Virus binds to a specific receptor and cell beings invagination (folding inward). b) Host cell membrane forms a pocket around the virus and it is internalized in an endosome. B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration): 2. Receptor-Mediated Endocytosis * Key steps in receptor-mediated endocytosis: d) Release of viral genome to cytoplasm varies between enveloped and non-enveloped viruses. * Enveloped viruses: Viral fusion proteins trigger fusion between the viral envelope and endosomal membrane. * Non-enveloped viruses: Acidification triggers pore formation or capsid destabilization, allowing the viral genome to escape into the cytoplasm B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration): 3. Direct Penetration Direct penetration is a viral entry mechanism used exclusively by non-enveloped viruses. Non enveloped virus used specialized capsid proteins to puncture, destabilize, or form pores in the host cell membrane. The viral genome to enter the cytoplasm directly. B. Viral Entry (Penetration) and Uncoating Mechanisms of viral Entry (Penetration): 3. Direct Penetration * Key steps: c) Viral genome (RNA or DNA) is injected through the pore directly into the cytoplasm. — The capsid often remains outside or partially attached to the cell surface. — No endosome or acidification step is involved B. Viral Entry (Penetration) and Uncoating Mechanisms of viral uncoating: © Uncoating is the process where the viral capsid is removed, releasing the genome for transcription/replication. © The main goal is to expose the viral genome to host cell machinery. © Uncoating is highly regulated; 1. If is too early, the viral genome is destroyed host cell. 2. If it is too late, viral replication is delayed B. Viral Entry (Penetration) and Uncoating Mechanisms of viral uncoating: I. Uncoating at the Plasma Membrane: 1. Occurs simultaneously with membrane fusion. 2. Envelope merges with host membrane & capsid released. 3. Capsid undergoes disassembly in the cytoplasm: Example; 1. HIV undergoes partial uncoating shortly after fusion. 2. Dengue virus: E protein rearranges in acidic endosome B. Viral Entry (Penetration) and Uncoating Mechanisms of viral uncoating: ITI.Multi-Step/ Sequential Uncoating: © Some viruses uncoat in stages e.g. HIV. © Mechanism: 1. Partial uncoating in cytoplasm. 2. Core transported along microtubules. 3. Reverse transcription within capsid. 4 Final uncoating at nuclear pore B. Viral Entry (Penetration) and Uncoating Factors affecting Viral Entry and Uncoating: |sino_|category _____—| Regulatory Factor_| RoleinEntry&Uncoating Mediate membrane fusion in enveloped viruses. Fusion proteins Activated by receptor binding or low pH. 1 | Viral Factors Determines when and where the capsid dsassembles: Capsid stabity ~Too stable = blocked entry - Too unstable = premature uncoating Ton channess (e.g., Influenza M2) | Regulate internal virion pH to trigger uncoating inside the endosome. ‘Acidification triggers conformational changes in vial proteins, fusion, or Endosomal pH capsid weakening. Activate viral proteins or cleave capsid components to promote Proteases (cathepsins) umncoot, Required for viruses that must transport their genome or core to the "Nudear import machinery nuckus (e.g., DNA viruses). Affects vial stabity and rate of conformational changes needed for Temperature erty. 3 | Environmental Factors | pH Influences vial protein structure and membrane fusion efficiency. Bock receptor binding, fusion, ion channeés, or protease activity; Inhibitors (drugs, antibodies) prevent successfl crtry/urepoting STEP 3: REPLICATION OF VIRAL GENOME Cc. Viral Genome Replication O This is the process through which viruses make copies of their nucleic acid genomes inside host cells. O Principles of viral genome duplication Viruses rely on host cel machinery (nucleotides, enzymes, energy). Host Dependency DNA viruses often use host polymerases (except large ones lke poxviruses). RIA viruses must encode RNA-dependent RNA polymerases (RdRp). (+)ssRNA can be directly translated. Genome Polarity Matters (-)ssRNA and dsRNA require RdRp to synthesize mRNA first. DNA viruses repicate in the nucleus (except poxviruses which replicate in the Replication Occurs in Specific | cytoplasm). Compartments, RNA viruses mostly replicate in the cytoplasm (except influenza, bomavirus). RdRp lacks proofreading thus leading to rapid viral evolution, quasispecies formation. High Mutation Rates in RNA Viruses DNA viruses mutate slowly because of proofreading. Template—Product New genomes are synthesized using the old genome as a template, following base- Complementarity Pairing rules. Cc. Viral Genome Replication © The mechanism of genome duplication in viruses is classified into three groups based on genome type: A. DNA genome replication B. RNA genome replication, and C. Reverse-transcription-based replications O Each category employs distinct enzymatic strategies and replication intermediates. Cc. Viral Genome Replication Viral DNA genome replication U This is a process through which DNA viruses synthesize new copies of their genomes inside host cells. © The mechanism of duplication depends on; 1. Genome structure (ssDNA or dsDNA, circular or linear) and 2. Whether the virus uses host or viral polymerases. C. Viral Genome Replication Viral DNA genome replication © Steps of semi-conservative replication viral replication include 1. Unwinding of DNA by helicase 2. DNA polymerase uses each strand as a template for making a new complementary strand . 3. Each double-stranded DNA consists of: 1. One parental strand (original). 2. One daughter strand (newly synthesized). 1 NB: After replication, no DNA molecule is completely “new." Instead, each contains half old and half new material. C. Viral Genome Replication Viral DNA genome replication © Steps of DNA viral replication include 5. DNA synthesis: * Leading strand: continuous (5’ > 3’) * Lagging strand: discontinuous, Okazaki fragments (3’ > 5‘). 6. Genome amplification (bidirectional forks or strand-displacement). 7. Late gene expression of structural proteins for assembly. 8. Packaging of replicated genomes into capsids.. C. Viral Genome Replication Viral DNA genome replication © Steps of replication of viral DNA include; 1. Attachment & Entry and genome delivered to nucleus (most). 2. Early gene expression involving synthesis of replication proteins. 3. Origin recognition by viral or host proteins. 4. DNA unwinding by helicase. C. Viral Genome Replication Viral DNA genome replication © Replication mechanism of viral DNA-based genome vary with genome type; 1. ds DNA viruses * use host DNA-dependent DNA polymerase. * e.g. adenovirus. 2. Single-Stranded DNA (ssDNA) Viruses * Must first be converted to dsDNA by host enzymes. * Parvoviruses use a rolling-hairpin mechanism. * Circoviruses use rolling-circle replication mechanism 
