1. Introduction to Virology Casey D. Morrow, Ph.D. Department of Cell Biology caseym@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. http://www.bioteach.ubc.ca/MolecularBiology/AMonksFlourishingGarden/ The DNA -> RNA -> Protein Pathway RNA Polymerase = enzyme that makes mRNA from the DNA gene template

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/u2fig 2b.jpg http://www.tarvacin.com/media/gif/EnvelopedVirusStructure.gif

11. Icosahedral Capsid Assembly

12. Examples of Icosahedral Capsids 1.Equine Herpesvirus Nucleocapsid 2.Simian Rotavirus 3.Reovirus type 1 virion 4.Intermediate partice: Reovirus 5.Inner core particle (Reovirus) 6.Human Papillomavirus type 19 7.Mouse Polyomavirus 8.Cauliflower Mosaic Virus

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

14. Example Envelope Glycoprotein: Influenza Hemagglutinin

15. Steps of Virus Replication Cycle

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

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

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

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 ImmunopathogenesisImmune MediatorsExamples Flulike symptomsInterferon, cytokinesRespiratory viruses, arboviruses (viremia- inducing viruses) Delayed-type hypersensitivity and inflammation T cells, macrophages, and polymorphonuclear leukocytes Enveloped viruses Immune complex diseaseAntibody, complementHepatitis B virus, rubella Hemorrhagic diseaseT cell, antibody, complementYellow fever, dengue, Lassa fever, Ebola viruses Postinfection cytolysisT cellsEnveloped viruses (e.g., postmeasles encephalitis) Immunosuppression-Human immunodeficiency virus, cytomegalovirus, measles virus, influenza virus