1. Basic Viral Structure
2. Genetic Material
3. DNA Viruses: Single-stranded (ssDNA) or double-stranded (dsDNA).
4. RNA Viruses: ssRNA (positive-sense [+] or negative-sense [–]) or dsRNA.
5. Retroviruses: Enveloped ssRNA positive-sense viruses that reverse transcribe RNA into DNA (e.g., HIV).
6. Capsid
7. Protein coat protecting nucleic acid; composed of repeating protein subunits called capsomeres.
8. Capsid Symmetry:
9. Helical: Rod-shaped capsomeres form a helical tube (e.g., Tobacco mosaic virus).
10. Icosahedral: Spherical shape approximated by 20 equilateral triangular faces (e.g., Adenovirus).
11. Complex/Asymmetric: Combined icosahedral head and helical tail (e.g., bacteriophage T4). Some poxviruses have complex brick-shaped capsids.
12. Envelope (in some viruses)
13. Lipid bilayer derived from host cell plasma or organelle membranes during budding.
14. Contains viral glycoproteins (spikes) that mediate host cell recognition and membrane fusion.
15. Enveloped viruses (e.g., influenza, HIV, herpesviruses) are generally more sensitive to detergents and desiccation than naked viruses.
16. Non-Enveloped (Naked) Viruses
17. Lack an envelope; more resistant to environmental conditions (pH, detergents).
18. Entry typically via receptor-mediated endocytosis or direct penetration.

1. Classification of Viruses

Viruses are classified based on:

1. Type of Nucleic Acid
2. DNA vs. RNA; single-stranded vs. double-stranded; positive vs. negative sense for ssRNA.
3. Capsid Symmetry
4. Helical, icosahedral, or complex.
5. Envelope Presence
6. Enveloped vs. non-enveloped.
7. Genome Segmentation
8. Some viruses have segmented genomes (e.g., Influenza A has eight RNA segments), enabling reassortment.
9. Replication Strategy (Baltimore Classification)
10. Group I: dsDNA → mRNA (e.g., Herpesviridae).
11. Group II: ssDNA → dsDNA intermediate → mRNA (e.g., Parvoviridae).
12. Group III: dsRNA → mRNA (e.g., Reoviridae).
13. Group IV: (+) ssRNA → mRNA (directly serves as mRNA; e.g., Togaviridae).
14. Group V: (–) ssRNA → (+) mRNA (requires RNA-dependent RNA polymerase; e.g., Orthomyxoviridae).
15. Group VI: (+) ssRNA with reverse transcriptase → DNA intermediate → mRNA (Retroviridae).
16. Group VII: dsDNA viruses with reverse transcriptase (e.g., Hepadnaviridae).

1. Viral Replication Cycles

Although specifics vary, most viral life cycles involve:

1. Attachment
2. Binding of viral surface proteins (capsid or envelope glycoproteins) to specific host cell receptors (proteins, glycoproteins, carbohydrates).
3. Tropism: Virus can infect only cells expressing the appropriate receptor(s).
4. Entry (Penetration)
5. Naked viruses: Often enter via receptor-mediated endocytosis, then uncoat in endosomes.
6. Enveloped viruses:
7. Fusion with plasma membrane (e.g., HIV gp41–gp120 complex) releases nucleocapsid into cytoplasm.
8. Endocytic entry: After endocytosis, low pH in endosome triggers envelope fusion.
9. Uncoating
10. Release of viral genome (and some viral proteins) into host cytoplasm or nucleus.
11. Genome Replication and Transcription
12. DNA Viruses: Most replicate in host nucleus using host DNA polymerases (except poxviruses, which replicate in cytoplasm using viral polymerases).
13. RNA Viruses:
14. (+) ssRNA: Viral RNA acts directly as mRNA; ribosomes translate viral proteins, including RNA-dependent RNA polymerase (RdRP) to replicate genome.
15. (–) ssRNA: Viral RdRP packaged in virion synthesizes complementary (+) mRNA and replicates genome.
16. Protein Translation and Processing
17. Early (Immediate) Proteins: Regulatory proteins that modulate host environment, counteract host defenses, and prepare for genome replication.
18. Late Proteins: Structural proteins forming capsid, envelope glycoproteins.
19. Post-translational modifications (glycosylation, cleavage by host/viral proteases).
20. Assembly (Maturation)
21. New viral genomes and capsid proteins assemble into nucleocapsids.
22. Envelope glycoproteins are inserted into host cell membranes (plasma or organelle membranes).
23. Release
24. Budding: Enveloped viruses bud through host membrane (plasma, endoplasmic reticulum, or Golgi), acquiring envelope and glycoproteins. Budding may or may not kill the cell.
25. Lysis: Non-enveloped viruses often cause cell lysis to release progeny; host cell membrane ruptures.

1. Lytic vs. Lysogenic Cycles (Bacteriophages)
2. Lytic Cycle:
3. Attachment to host cell surface.
4. Injection of phage DNA into cytoplasm.
5. Phage DNA directs host machinery to replicate viral components.
6. Assembly of phage particles.
7. Release of new phages by lysis of host cell.
8. Lysogenic (Temperate) Cycle:
9. Phage attaches and injects DNA.
10. Phage DNA integrates into host chromosome (prophage).
11. Host replicates normally, copying prophage DNA to daughter cells.
12. Under induction (stress), prophage excises and enters lytic cycle.

1. Viral Pathogenesis and Host–Virus Interactions
2. Host Range and Tissue Tropism
3. Determined by receptor compatibility, intracellular factors, and immune evasion strategies.
4. Example: HIV infects CD4⁺ T lymphocytes, macrophages (requires CD4 receptor and CCR5/CXCR4 coreceptors).
5. Host Immune Responses
6. Innate Immunity: First line of defense—interferons (IFN-α, IFN-β) produced by infected cells, activating antiviral states in neighboring cells; natural killer (NK) cells lyse infected cells.
7. Adaptive Immunity:
8. Humoral (B cell) Response: Production of neutralizing antibodies targeting viral capsid or envelope proteins; preventing viral entry.
9. Cell-Mediated (T cell) Response:
   • CD8⁺ cytotoxic T lymphocytes recognize peptide–MHC class I complexes on infected cells, inducing apoptosis.
   • CD4⁺ helper T cells coordinate immune responses.
10. Viral Evasion Strategies
11. Antigenic Variation: Frequent mutations in viral surface proteins (antigenic drift in influenza) or genome segment reassortment (antigenic shift), evading antibody recognition.
12. Latency: Some viruses (e.g., herpesviruses) remain dormant within host cells (e.g., neurons), periodically reactivating under stress.
13. Downregulation of MHC: Viruses interfere with antigen presentation (e.g., cytomegalovirus reduces MHC I expression).
14. Inhibition of Apoptosis: Viral proteins (e.g., baculovirus p35) block host cell apoptosis to prolong replication period.

1. Viruses in Evolution and Ecology
2. Horizontal Gene Transfer (HGT)
3. Viruses can facilitate gene transfer between unrelated species (transduction in bacteria; viral vectors in eukaryotes).
4. Genetic material from viruses (endogenous retroviruses) comprises significant proportions of eukaryotic genomes (e.g., ~8% of human genome), influencing genome architecture and regulation.
5. Viral Ecology
6. Viruses regulate population dynamics of microbial communities (phages controlling bacterial abundance in aquatic ecosystems).
7. Viral shunt: Viral lysis releases organic matter, fueling microbial loop in marine environments.
8. Co-evolution
9. Arms race between host immune defenses and viral countermeasures drives rapid evolution in both.
10. Red Queen hypothesis: Continual adaptation required by both host and virus to maintain status quo.