Viruses: intimate parasites

1. Viruses: intimate parasites • Are viruses alive? • Not made of cells, in violation of Cell Theory • Do not grow(but self assemble) • Do not metabolize(but steal energy) • Cannot reproduce w/o a host cell(but other organisms may require another species in order to reproduce) • Can evolve over time • Some can respond to environmental stimuli • Have a complex, organized structure

2. If not cells, then what? • Viruses are particles • Some components are essential • A genetic material with the blueprint for making more • Could be: ds DNA, ss DNA, ss RNA, ds RNA • Space is limited, so genes are few • A covering to protect the genetic material • Capsid, made of one or more proteins • Capsid + nucleic acid: nucleocapsid • Viruses are obligate intracellular parasites

3. Viruses may have other parts • Envelope: piece of organelle membrane or cell membrane covering capsid • Virus is formed by budding, pushes through membrane taking a piece. • Viral envelope usually contains viral proteins. • Envelope makes virus susceptible to some disinfectants • Spikes (peplomers) extend from envelope • Used for attachment, escape • Accessory enzymes • Reverse transcriptase, RNA RNA enzymes

4. Viral size and shape • Viruses range from 20 nm to 300 nm • Ribosomes are about 30 nm • The smallest known bacteria are about 200 nm • Viral shapes: • helical, polyhedral, and complex http://www.glencoe.com/qe/images/b136/q4323/ch18_0_a.jpg; www.blc.arizona.edu/.../ Figures/Icos_Virus.GIF; http://www.foresight.org/Updates/Update48/Images/T4Schematic.jpg

5. Examples of virus shapes Ebola Adenovirus http://www-cgi.cnn.com/HEALTH/9604/16/nfm/ebola.levine/ebola.reston.large.jpg; http://www.virology.net/Big_Virology/EM/Adeno-FD.jpg

6. Specificity • A recurring theme in biology: • Enzymes, membrane receptors, antibodies, etc. • Viruses are limited to certain types of host cells • Species barriers: rabies not specific, but most are • Tissue type: rabies specific to nerve, salivary tissue • Cell type: HIV infection mostly restricted to Helper T cells, a kind of lymphocyte. • Different characteristics of host cells involved • Attachment to cell surface often a major point • Every type of organism has a virus that infects it?

7. Viruses across kingdoms • A densovirus newly isolated from the smoky-brown cockroachPeriplaneta fuliginosa • Acanthamoeba castellanii Promotion of In Vitro Survival and Transmission of Coxsackie B3 Viruses • The causal organism is the Tulip Breaking Virus (TBV). The pathogen is a potyvirus and is divided into two strains, • Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus

8. Classification • Microbes problematic, viruses especially so. • No sexual reproduction, no asexual reproduction, just “assembly”. • No clear evolutionary relationships • Classification scheme (from David Baltimore) • First, by nucleic acid type, e.g. ds DNA, + sense RNA • Next, structural characteristics (presence of envelope, capsid shape), type of organism infected, etc.

9. Life cycle of a virus • Manner of infection and reproduction depends on whether host is prokaryotic or eukaryotic. • Life cycle here outlined is general: • ADSORPTION: following contact, molecules on surface of virus bind to particular molecules on host cell. • PENETRATION: the nucleic acid must get access to the machinery of the cell to replicate. http://www.tthhivclinic.com/Fig_20.gif

10. Life cycle continued • SYNTHESIS/REPLICATION: once inside the nucleic acid issues orders leading to • Replication of the nucleic acid • Transcription (usually) and translation, producing the necessary capsid proteins. • ASSEMBLY: a spontaneous process • Capsid proteins and nucleic acid combine to make virion. • Cheap but highly inefficient process. • RELEASE: successful parasite must spread to others • Virus causes lysis of cell or pushes through cell membrane. Virions may acquire an envelope.

11. Bacteriophage: lytic vs. lysogenic • Most bacteriophages multiply then lyse the host cell • This life cycle is called a lytic cycle • Others are “temperate”, enter a lysogenic cycle. • Lysogeny is an effective way to multiply the viral DNA • Viral DNA inserts into the bacterial chromosome • Now called a “prophage” • Bacterial replication also replicates viral DNA • Prophage may bring new genes for use by bacterium • Damage to bacterial DNA (e.g. UV) prompts virus to begin lytic cycle; DNA excises, virus multiplies.

12. Measuring numbers of virions:the Plaque Assay • Virus and host cells are mixed • Bacteria cover in a Petri dish as a “lawn”, eukaryotic cells cover bottom of a dish. • Multiplication of virus leads to release, spread to and destruction of nearby cells. • Visible as holes, plaques, on bacterial lawn; eukaryotic cells in culture are first stained for easier view to see plaques. http://dept.kent.edu/biology/Courses/30171/imageQBT.JPG;news.bbc.co.uk/.../ _230333_cell_culture_300.jpg;

13. Growing viruses • Obligate intracellular parasites: require a host cell!! • Whole organism • Animal models, human volunteers • Ethically, humans require consent, safety, pay • Eggs: aseptic incubator • Various cells and membranes support growth of viruses • Shell provides protection from bacterial contamination • Used for large batches of viruses for vaccines • Egg allergies a problem sometimes http://www.fao.org/ag/againfo/foto/egg-facts.gif

14. Growing viruses continued • Organ/tissue/cell culture • Minced tissue, separated into cells by enzyme treatment • Grown in sterile plastic dish with nutrient solution • Cells prepared this way grow until dish is covered, stop. • Scrape up, use some to inoculate new culture • Limited number of rounds of replication • Transformed cells, with cancer properties, grow forever. • Must be subcultured when dish bottom is covered • Cell culture major reason for advances in virology

15. Viruses and disease • Most of discomfort, some of damage, is due to host defense response to viral infection. • Cytopathic effects: damage caused by viruses • Cells change shape, change size (round up, swell) • Cells become sticky (clump, fuse to form syncytia) • Syncytia are giant, multinucleated cells • Cells change internally (vacuoles, inclusions) • Location, appearance of inclusions characteristic of certain viruses; comprised of viral parts or cell debris • Cells die.

16. Other effects of viruses • Transformation: cells become cancer-like • Lose contact inhibition • Continue to multiply • In vivo, produce tumors • Certain Herpes-type viruses, genital wart virus, etc. • Some viruses cause birth defects = teratogenesis • Damage to critical cells in fetus, failure to form parts • Typically, virus is mild and able to cross placenta • Rubella (German measles virus), CMV

17. NOT viruses • Viroids: naked RNA • Cause of infectious disease in plants • Prions: infectious protein particles • Got Stanley Prusiner the Nobel Prize, but still controversial. • Cause of Mad Cow Disease, Scrapie, Elk Wasting disease, Creutzfeldt-Jakob disease, Kuru, etc. • Transmissible spongioform encephalopathies • Misshapen protein causes normal protein to also fold incorrectly, increasing their numbers • Replication without the presence of nucleic acid

18. Prions Normal cell protein Misfolded version: prion www.stanford.edu/.../2004anderson/index.html

19. Attack and defense • Virus has ways of attacking • Specific binding to host cell receptor • Receptors involved in normal cell functions • Virus may regulate cell division for its own replication • Insertion of viral DNA into chromosome allows virus to hide from immune system • Causes adjacent cells to fuse, allows cell to cell spread without leaving cell.

20. Defense by host • Host has ways of defending • Cell mediated immunity (T cells): infected cells killed. • Antibodies intercept virions between cells, in fluids • Interferon produces anti-viral state, prevents replication • Natural killer cells act • Using antibodies as tags • Quickly before B &T cells ready

21. Pathogenic Viruses • Name of virus • what family it belongs to • what disease it causes, organ system affected • DNA or RNA? • Route of transmission; reservoirs, vectors • Viral virulence factors (selected viruses) • Immunizations

22. A molecular biology lesson • RNA mutates more readily than DNA • Copying mistakes by the enzymes are not corrected • Not double stranded, so no mismatches noticed that can be fixed. • Many variants result • Less chance of lasting immunity • Harder to create vaccines

23. HIV: Human Immunodeficiency Virus • Host range • Main types of cells infected: T helper cells and dendritic cells (including macrophages, microglia) • Have CD4 and CCR5 glycoproteins on surface • Infection process • RNA is copied into cDNA by reverse transcriptase • cDNA inserts into host chromosome • New RNA made • Protein precursor made, then processed; assembly occurs • Virions bud through cell membrane

24. HIV life cycle • Binding to host cell • Copying RNA into DNA by Rev Trans • Integration into host DNA • Transcription • Translation • Assembly and exit by budding www.aidsmeds.com/images/HIVLifeCycle1.gif

25. Disease process • Chronic infection • T cells continually made, continually destroyed • Eventually, host loses • AIDS diagnosis: • Acquired Immuno Deficiency Syndrome • CD4 cell count below 200/µl; • opportunistic infections • Examples of opportunistic “infections” • Pneumocystis carinii pneumonia (PCP pneumonia) • Kaposi’s sarcoma; Tuberculosis; several others

26. Prevention and Treatment • Prevention is easy • Practice monogamous sex, avoid shared needles • HIV cannot be spread by casual contact, skeeters • Drug treatment • Nucleoside analogs such as AZT • Protease inhibitors prevent processing of viral proteins Nifty animation at: http://www.hopkins-aids.edu/hiv_lifecycle/hivcycle_txt.html