Importance of Viruses

1. Cause many diseases in plants, animals & humans Some viruses are easily controlled with a vaccine Mumps, Measles, Smallpox, Polio Some viruses are difficult to control with a vaccine Retroviruses (HIV: ssRNA  dsDNA) Common cold, Influenza (Flu), HIV Used as vectors in biotechnology Used to insert therapeutic genes into a host cell chromosome Use viruses with provirus in life cycle Importance of Viruses

2. Herpes(dsDNA  dsDNA) Cold sores Herpes virus may rest inactive inside host cells for long periods

3. Adenovirus (dsDNA) Adenoviruses cause various respiratory diseases

4. Polio Virus(ssRNA serves as mRNA) Polio is easily prevented with a vaccine

5. Measles(ssRNA template for mRNA synthesis) Measles: a childhood disease that can be prevented with a vaccine

6. Couple at AIDS quilt (HIV: ssRNA  dsDNA) HIV is very difficult to control with a vaccine

7. 1918 Influenza epidemic(ssRNA template for mRNA synthesis) >20 million died of the flu during WW I A new influenza vaccine must be developed yearly

8. Influenza Today

9. Enter H5N1, the avian flu virus

15. Why do new strains of influenza and bird flu arise in Asia?

16. Background: Influenza Virus Structure (1 of 3) • Flu viruses are named by the type of surface proteins • Hemagglutinin • Helps virus enter cell • Type A infects humans, birds and pigs • Type A has ~ 20 different sub types • Flu Viruses Currently infecting... • Humans: H1N1, H1N2, and H3N2 • Avian Flu Virus: H5N1

17. Background: Influenza Virus Structure (2 of 3) • Named for the type of surface proteins • Neuraminidase • Helps virus exit cell • 9 subtypes • Currently infecting Humans: • H1N1, H1N2, and H3N2

18. Background: Influenza Virus Structure (3 of 3) • Influenza viral genome • ssRNA • 8 segments (pieces) • One gene per segment • Avian Flu Virus: H5N1 • Transmitted from birds to humans • No evidence of human to human transmission • Antiviral drugs: Tamiflu • a neuraminidase inhibitor • Consequences of its action?

19. Antigenic drift – due to errors in replication and lack of repair mechanism to correct errors Results in ___________________ changes Antigenic shift - reassortment of genetic materials when concurrent infection of different viral strains occurs Results in ___________________ changes Genetic Changes in Influenza Viruses

20. Emergence of New Influenza Subtypes: H5N1 Antigenic shiftdue to genome reassortment within intermediate hosts drives flu epidemics and pandemics Solid lines: transmission demonstrated; Dotted lines: transmission postulated but not demonstrated. Source: http://www.cdc.gov/ncidod/EID/vol12no01/05-1024-G1.htm • Nonpathogenic H5 influenza virus: Wild fowl  domestic ducks and geese,  domestic chickens. • H5 virus became highly pathogenic in chickens  domestic ducks and geese. • Highly Pathogenic H5 virus reassorted its genome with those of other influenza viruses in aquatic birds,  spread to poultry farms, humans, and occasionally to pigs.

21. Where do the “new flu” viruses come from? Antigenic Drift:mutations result in changes to the Hemagglutinin (HA) molecules • - RNA replication is error prone • - New HA types are created frequently • Requires new vaccine every “season” • What is a vaccine?

22. What is a vaccine? Vaccines stimulate the production of memory cells Give long-term protection against a specific antigen Why are vaccines ineffective against the flu virus? Why will this year’s flu vaccine be ineffective next year? Why are vaccines effective against DNA viruses? e.g. small pox and polio virus Vaccines: Protection against viruses

23. Smallpox (dsDNA  dsDNA) Smallpox has been irradicated worldwide due to a very successful vaccine Why are vaccines for DNA viruses so successful?

24. Hepatitis B—an RNA virus Hepatitis B Infections may lead to liver cancer. Why? Carry viral oncogene

25. Tumor Viruses: may transform normal cells into cancer cells Hepatitis B Liver cancer HTLV 1 leukemia (Human T-Cell Leukemia Virus) Tumor viruses form a permanent provirus Viral oncogenes code for growth factors Growth factors Stimulate cell to enter S phase G1 or G0 S phase Each of the following must happen for cancer to occur Active host oncogenes + Active viral oncogenes  cancer Activators of host oncogenes Carcinogens, radiation, some viruses Viruses and Cancer

26. Emerging viruses Ebola Virus Hanta Virus Both viruses: ssRNA template for mRNA synthesis Either virus usually results in death within days!

27. Deer Mouse: Carries Hanta virus in Feces

28. Mottling of Squash and Tobacco by the Mosaic Virus Viruses can spread easily from cell to cell via the plasmodesmata junctions between cells

29. Tobacco mosaic virus (RNA virus)

30. Comparing the size of a virus, a bacterium, and a eukaryotic cell • Viral Size • Millions can fit on pinhead • Smaller than a ribosome!

31. Viral structure TMV Adenovirus Influenza virus Bacteriophage T4

32. Nucleic Acid + Protein Coat (Capsid) Some viruses with Membrane (envelope) surrounding capsid Envelope derived from plasma membrane of host cell Helps virus infect host cell No organelles Obligate intracellular parasite Lacks metabolic enzymes, ribosomes, mitochondria Alone, can only infect host cell Nucleic Acid: DNA or RNA Single or Double Stranded 4 genes to a few hundred Viral Structure

33. Classes of Animal VirusesGrouped by Type of Nucleic Acid

34. Host cell Recognition Complementary fit between external viral proteins and host cell surface proteins Some have a Broad host range Swine flu and rabies viruses Some have a narrow host range Single tissue in a single species e.g. Adenovirus, HIV Phages of E. coli Host Range

35. Simplified DNA Virus Life Cycle E.g. smallpox, herpes, chickenpox “Lock and Key” fit between viral surface proteins and host cell receptors initiates endocytosis Viral Reproduction

36. Electron micrograph of Bacteriophage T4 Bacteriophages are viruses that infects bacteria

37. Bacteriophages (Bacterial Viruses) Best understood of all viruses Responsible for many advances in molecular biology Hershey-Chase expmts that showed that DNA is the genetic material Restriction Enzymes used in Genetic Engineering come from bacteria Lytic Cycle of Bacteriophage T4 T4 is a Virulent Phage Lyses host  death of host cell Bacteriophage Reproduction

38. The lytic cycle of phage T4

39. Lytic and Lysogenic reproductive cycles of phage , a temperate phage What is the adaptive value of forming a prophage? Lysogenic Cycle Lytic Cycle Prophage

40. RNA viruses RNA serves as template to produce mRNA e.g. viruses that cause rabies, measles, mumps, flu DNA viruses DNA serves as template to produce mRNA Herpes (Cold sores, genital herpes) Smallpox Adenovirus The reproductive cycle of an enveloped Virus

41. AIDS: Acquired Immunodeficiency Syndrome • AIDS—caused by HIV infection • HIV = Human Immunodeficiency Virus HIV infecting a Helper T-Cell

42. HIV infection

43. AIDS around the world (Source: UNAIDS)

44. The Structure of HIV: A Retrovirus (RNA virus) Envelope protein Carbohydrate Lipid envelope Reverse Transcriptase Protein Capsid made of protein RNA (2 copies of its genome)

45. Animation of HIV Life Cycle Questions to Address: • Why does HIV infect a specific cell type, T-helper cells (CD-4 cells)? • What is HIV’s Genetic material? • What are the roles of Reverse Transcriptase, integrase, and protease? • How can knowledge of HIV’s life cycle be used to develop anti-HIV treatments? • Reverse Transcriptase does not “proof read” like DNA polymerase does. • What are the consequences? • Of what adaptive value is this?

46. HIV primarily infects T-Helper Cells! • Why does HIV have a narrow host range? • Why does the virus that causes rabies have a broad host range? 3.) Infection HIV 2.) Fusion 1.) Binding Envelope protein Capsid RNA CD4 Receptor protein Cytoplasm of white blood cell (T-Helper Cell) Helper protein Plasma membrane of T-helper cell

47. What’s happening? 1. 2. 3. 4. 5. 6. Reverse transcriptase Overview of HIV’s Reproductive Cycle DNA of host cell Viral RNA Provirus DNA 1 DNA strand Nucleus 2 Double-stranded DNA 3 4 5 Viral RNA and proteins Cytoplasm 6

48. Reproductive Cycle of HIV—the details! HIV Entry Reverse transcriptase Viral RNA Viral RNA copied to viral DNA Integrase Viral DNA integrates into cell chromosomes andmakes more viral RNA Viral RNA Synthesis of HIV proteins Protease cleaves large proteins into smaller ones HIV envelope proteins come to cell surface HIV assembles and buds from cell

49. Treatments for HIV • Vaccines have beenunsuccessful—why? • Reverse Transcriptase Inhibitors Block viral DNA formation from viral RNA • DNA base analogs Block DNA elongation • e.g. AZT, 3TC (3-thiocytosine) • Protease Inhibitors Block enzymes that process envelope proteins • Why use a “Shotgun” approach? • Possible future treatments: • Plug drugs—drugs that plug receptors for HIV on surface of host cell • Vaccines

50. Evolved from fragments of Cellular Nucleic Acids Evidence Viral genetic material similar to host cells genetic material Some viral genes are identical to host’s genes Eukaryotic viral genetic material is quite different to prokaryotic and phage genetic material Eukaryotic viral genetic material is similar to transposons (“jumping genes”) Transposons: highly mobile eukaryotic genetic material Phage DNA is similar to Plasmid DNA Plasmid DNA: highly “mobile” extra-chromosomal circular DNA found in bacteria Evolutionary Origin of Viruses