Introduction to Virology Casey D. Morrow, Ph.D. Department of Cell Biology caseym@uab.edu

1. Introduction to VirologyCasey D. Morrow, Ph.D.Department of Cell Biologycaseym@uab.edu • Viral replication: How viruses exploit cells to make new viruses • Viral pathogenesis: How virus replication causes disease and how viruses escape/interact with the immune system

2. The DNA -> RNA -> Protein Pathway RNA Polymerase = enzyme that makes mRNA from the DNA gene template http://www.bioteach.ubc.ca/MolecularBiology/AMonksFlourishingGarden/

3. Characteristics of Viruses • “Filterable agents” – Pass through filters that capture bacteria • Obligate intracellular parasites • Minimal genetic information, efficient • Rely on host cell machinery to fulfill replication cycle • Assembled from building blocks encoded by the virus (don’t divide like cells) • Absolutely require host cell for replication to produce proteins required to synthesize new viral genomes and the building blocks of the virus structure

4. For a Virus to be Successful: • Capable of transmission through potentially harsh environmental conditions • Traverse skin or other barriers of the host • Must adapt to the biochemical machinery of the host cell for replication • Escape elimination by the host immune response

5. Basic Components of a Virion

6. Virus Classification • Size • Morphology • Genome Type (DNA or RNA) • Means of Replication

7. Relative Sizes of Viruses

8. General Structure of Viruses

9. Genome Contents of Viruses • RNA • Single-strand • Double-strand • Linear • segmented • DNA • Double-strand • Single-strand • Linear • Circular http://gsbs.utmb.edu/microbook/images/fig41_6.JPG

10. Naked vs. Enveloped Viruses • Naked Capsids • Withstand harsh environmental conditions • Resistant to drying, acids, detergents • Many are transmitted fecal-oral route • Enveloped Viruses • Can’t dry out • Not stable in acid • General must remain in body fluids (respiratory, blood) http://www.cat.cc.md.us/courses/bio141/lecguide/unit2/viruses/images/u2fig2b.jpg http://www.tarvacin.com/media/gif/EnvelopedVirusStructure.gif

11. Icosahedral Capsid Assembly

12. Examples of Icosahedral Capsids • Equine Herpesvirus Nucleocapsid • Simian Rotavirus • Reovirus type 1 virion • Intermediate partice: Reovirus • Inner core particle (Reovirus) • Human Papillomavirus type 19 • Mouse Polyomavirus • 8. Cauliflower Mosaic Virus

13. General Enveloped Virus Structure Influenza HIV http://www.schoolscience.co.uk/content/5/biology/mrc/hiv/page2.html

14. Example Envelope Glycoprotein: Influenza Hemagglutinin

15. Steps of Virus Replication Cycle

16. Recognition of Cells and Attachment HIV Sialic acid: bound by Influenza virus

17. Steps of Virus Replication Cycle Cell Entry: Naked Viruses: Typically endocytosis Enveloped Viruses: Typically cell fusion

18. Synthesis of New Viral Components • Viral Nucleic Acids • mRNA’s encoding viral proteins • New viral genomes for encapsidation into new virions (viral particles) • Viral Proteins • Enzymes and other proteins required for viral transcription and genome replication • Structural proteins (capsid proteins, viral glycoproteins)

19. The DNA -> RNA -> Protein Pathway RNA Polymerase = enzyme that makes mRNA from the DNA gene template http://www.bioteach.ubc.ca/MolecularBiology/AMonksFlourishingGarden/

20. DNA Virus Transcription • Generally use the host cell’s DNA-dependent RNA Polymerase II to make mRNA’s • Generally the DNA genomes go to the nucleus (some integrate into chromosomal DNA) • One exception: Poxvirus family – Replicates only in the cytoplasm of cell so can’t use host cell’s RNA Polymerase II; instead, makes its own enzymes for transcription of mRNA’s

21. RNA Virus Transcription • Many replicate entirely in the cytoplasm of the cell • Must encode their own enzymes (RNA-dependent RNA polymerases) for transcription of mRNA and to replicate their full-length RNA genomes • REASON: The host cell has no enzymes for generating new viral RNA genomes using an RNA template • PLUS-STRAND RNA VIRUSES: Genomes same sense as mRNA • MINUS-STRAND RNA VIRUSES: Genomes opposite sense as mRNA

22. Replication of Viral Genomes • DNA Viruses: • DNA-dependent DNA polymerases to make new DNA copies from DNA templates • Some use cellular DNA polymerases • Others encode their own DNA polymerases • RNA Viruses: • Use RNA-dependent RNA polymerases to make new RNA copies from RNA templates • Encoded by the virus • Plus-strand versus minus-strand • Retroviruses (example: HIV): • Genome in the viral particle is single-strand RNA • Packages Reverse Transcriptase • RNA  DNA  Integrated into chromosomal DNA • New viral RNA genomes transcribed in the nucleus by host cell polymerase

23. Viral Protein Synthesis • All viruses depend on host cell translation machinery (ribosomes, tRNA, post-translational modifications) to generate viral proteins from mRNA templates • Different strategies for compactness/efficiency: • Separate mRNA’s for each viral protein • Polyprotein strategy • Multiple proteins encoded on one mRNA • Individual proteins are derived from polyprotein by enzymatic cleavages catalyzed by proteases

24. Polyprotein Strategy

25. Assembly and Release • Enveloped Viruses: typically exit by budding from the cell • Naked viruses: typically exit through cell lysis

26. Lytic Virus Growth Curve

27. Viral Budding from Cell Membrane HIV budding from a cultured lymphocyte Budding Influenza Virus http://www.itech.pjc.edu/fduncan/mcb1000/micc6ppt_files/slide0004_image012.jpg http://en.wikipedia.org/wiki/AIDS http://www.med.wayne.edu/immunology/department/roberts2.html

28. Viral Pathogenesis • Interaction between the virus and the host • General Steps: • Entry into the body (ex. Fecal-Oral, Inhalation) • Primary Site of Replication • Viremia • Secondary Site of Replication in target tissues

29. Example: Ebola Primary Target Secondary Targets

30. Outcomes of Virus Infection at the Cellular Level • Failed infection (abortive) • Cell death: • Lytic viruses • Apoptosis (programmed cell death) • Infection without cell death • Chronic infection: no cell lysis, new viruses are produced • Latent infection: limited production of viral components; no new viruses produced • Cellular properties may change later resulting in viral production (ex. Herpes Simplex Virus) • Transformation: Virus infection results in cell immortalization (conversion to a tumor cell) • Oncogenic viruses

31. Host Defenses Against Viruses • Natural Barriers of the Body (ex. Skin) • Innate Immune Defenses (not antigen dependent) • Interferon response • Macrophages • Dendritic cells • Natural Killer Cells • Antigen-specific immune responses • Antibodies • Helper T-cells • Cell-mediated immunity • Recognition of virus-infected cells • Lysis of infected cells

32. Viral Strategies to Evade Host Defenses • Preventing interferon action: • Presence of double-stranded RNA in cell causes interferon response • Shuts down cellular translation (suspended animation) • Degradation of viral RNA • Changing viral antigens • High error-rate in many viral polymerases • Allows rapid change of protein sequences and, therefore, antigenic characteristics • Cell-to-cell spread: Evade antibodies • Suppression of antigen presentation and lymphocyte function (hide from immune system)

33. Viral immunopathogenesis