Virology

1. Virology

2. Cells • A living cell is a self-reproducing system of molecules held inside a container • The “container” is the plasma membrane (permeability barrier)

3. Eubacteria Archae- bacteria Protista Plantae Fungi Animalia BACTERIA ARCHAE EUKARYA Common Ancestor SIX KINGDOMS THREE DOMAINS

4. Unity All cells have similar basic chemistry Similar Metabolism

5. Unity • All cells must: - Obtain and utilize energy • - Maintain integrity (i.e. boundary between inside and out) • - Sense and respond to their environment • - Reproduce

6. Eubacteria Archae- bacteria Protista Plantae Fungi Animalia BACTERIA ARCHAE EUKARYA Common Ancestor SIX KINGDOMS THREE DOMAINS VIRUSES ????

7. Viruses are pieces of RNA or DNA enclosed in a protective protein coat, • which sometimes can be further surrounded by a lipid-based membrane. • They are the simplest of parasites, having evolved to reproduce inside, and survive outside, the cells they infect. What the hec is a virus?

8. One of the most amazing features of viruses is that they can do so much with so little: For example one of the world’s most deadly pathogens, hepatitis B virus, kills over a million people each year of liver disease yet it has only 4 genes!

9. Three Problems Every Virus Must Solve Viruses come in different shapes and sizes, but regardless of which virus we are studying all of them must solve three basic problems: Reproduce during its “visit” inside its target cell Spread from one individual to another 3) Evade host defenses

10. Three Problems Every Virus Must Solve • 1) Reproduce during its “visit” inside its target cell: • No virus carries with it the machinery required to synthesize proteins (e.g. ribosomes) • No virus can generate the energy (e.g. ATP) needed to power the copying of its genetic information and make viral components. • Therefore, viruses must “hijack” some of the biosynthetic machinery of the cells they infect and turn these cells into “viral factories”.

11. Three Problems Every Virus Must Solve • 1) Reproduce during its “visit” inside its target cell: • Viruses must have at least two plans: • 1) one for copying their genetic information • 2) another one for producing the messenger RNA that will encode the viral proteins. The strategies used by different viruses are quite diverse, and are influenced by the nature of the genetic material (DNA viruses vs RNA viruses), as well as by the types of cells they infect.

12. Three Problems Every Virus Must Solve • 2) Spread from one individual to another: • First the virus needs to be physically transported from one host to the next (transmission) i.e. through coughing, sneezing, etc. • Second, once they arrive to the new host, viruses must locate cells in which they can reproduce efficiently (not just any cell will do) i.e. cell must have surface receptors to which the virus can attach i.e. the biosynthetic machinery of the cell needs to be compatible with the replication strategy used by the virus • Only a few cell types in our bodies will have all the requirements for any given virus

13. Three Problems Every Virus Must Solve • 3) Evade host defenses: • Several mechanisms have been evolved by viruses to do this, some are very primitive, some very elaborate (we’ll talk more about this later). • It is important to understand that viral evasion of host defenses need not be complete. In fact, if a virus were to reproduced unchecked, it would probably kill the host before it could spread to another human. • A virus should elude the host’s anti-viral defenses at least long enough for it to reproduce in host number 1 and spread to host number 2, or to establish a latent or chronic infection within the original host from where to spread at a later time.

14. Three Problems Every Virus Must Solve 1) Reproduce during its “visit” inside its target cell 2) Spread from one individual to another 3) Evade host defenses • Finally, the solutions to these three problems of reproduction, spread, and evasion must be consistent. For example, it would not make much sense for a virus that reproduces only in liver cells to be spread by coughing. • Thus, the solutions to the three problems must fit together in an overall plan of infection

15. Viral Pathogenesis • Most human viruses cause some form of disease in their hosts, although some of these pathological conditions affect only a small subset of infected humans, or are so mild as to be virtually undetectable. • Think about it: it isn’t in the best interest of a virus to make its humans host ill, it would be like “biting the hand that feeds you”. • Rather, the diseases that viruses cause are the (usually unintended) consequences of the way each virus has chosen to solve the three problems of reproduction, spreading and evasion. • Sometimes, the pathology results from direct viral action (e.g. killing infected cells) • Sometimes, the host’s immune reaction to the virus is the main cause of harm (i.e.” collateral damage”)

16. Interferons

17. INTERFERONS • Interferons are soluble proteins that play an important role as a first line of defense against viral infections. • IFNs are made by cells in response to viral infection, and are released into the surrounding medium (the infected cell will often eventually die as a result of the infection). • IFNs then bind to receptors on neighboring cells and induce transcription of approximately 20-30 genes, and this results in an anti-viral state in the target cells.

19. DIFFERENT TYPES OF INTERFERONS • TYPE I interferons • Interferon-alpha • is produced mainly by • virus-infected leukocytes. • Interferon-beta • is produced mainly by virus-infected fibroblasts, or virus-infected epithelial cells.

20. INTERFERONS • TYPE II interferons • Interferon-gamma: is produced by certain activated T-cells (e.g. TH1) and NK cells. • In lymphocytes, interferon-gamma is made in response to antigen (including viral antigens) or mitogen stimulation. • Interferon-gamma increases expression of class II MHC molecules on antigen-presenting cells and thus promotes presentation of antigens to helper T cells.

21. … back to viruses

23. Rhinovirus • A member of the Picornaviridae family (pico=small; RNA; virus) • The average American suffers from a rhinovirus infection about once per year, and roughly half of the cases of the “common cold” are caused by this virus. • The virus is non-enveloped (i.e. it has no lipid membrane, just a protein capsid surrounding the nucleic acid) and possesses a single-stranded RNA genome of positive polarity (i.e. positive-strand RNA genome). In positive-stranded RNA viruses, the viral genome has the viral genes already in an orientation that can be read by rybosomes

24. Three Problems Every Virus Must Solve Viruses come in different shapes and sizes, but regardless of which virus we are studying all of them must solve three basic problems: Reproduce during its “visit” inside a human cell Spread from one individual to another 3) Evade host defenses

25. Rhinovirus 1) Reproduce during its “visit” inside a human cell: Cellular molecule that serves as virus receptor Attachment Entry vRNA Translation of Polycistronic RNA Nucleus of cell vPolyprotein (later it is cleaved) vRNA (+) Genome replication Viral RNA-dependent RNA Polymerase cRNA (-) vRNA (+) Cellular vesicle Assembly of new viruses Cytoplasm of cell Exit (usually killing infected cell) and beginning of new cycle (i.e. infection of a new cell)

26. Rhinovirus 2) Spread from one individual to another: • The virus spreads mainly by coughs and sneezes • Because of the structure of its protein capsid, rhinoviruses are most infectious at temperatures that are somewhat below normal body temperature • Favorite temperature for the virus: 91o F, • which just happens to be similar to that of the nose and upper airways! • Rhinovirus causes only acute infections (no persistence or latency)

27. Rhinovirus • 3) Evade host defenses: • Ciliated epithelia and mucus (“mucociliary escalator”) in the upper respiratory tract has a downward direction from the nasal cavity towards the throat to swallow and destroy in the stomach any incoming particle. • Rhinovirus uses this “escalator” to catch a “free ride” to the interior of the nasal cavity where the temperature is just right for optimal infection (of course if it goes too far it gets destroyed by low pH in the stomach). • Interferons: Rhinovirus disrupts the cellular machinery that secretes interferons -->low amounts of IFN a and b are produced and neighboring cells are not alerted of the presence of the virus. • The innate immune system is our main weapon against rhinoviruses (e.g. complement, professional phagocytes, and natural killer cells) and infections are over in just a few days, before the adaptive immune response kicks in.

28. Rhinovirus • 3) Evade host defenses: • Because the virus “surrenders”so quickly to your immune system, you do not develop good neutralizing antibodies (or large quantities of them) and are not well-protected in case of re-infection. • Also, the viral RNA polymerase that replicates the viral genome is error prone (i.e. it makes lots of mistakes while copying the viral RNA), therefore, an infected cell produces thousands of viruses that have the potential of carrying mutations. • The generation of mutant forms of the virus as it replicates is called “antigenic drift”, and can help rhinovirus evade the already weak adaptive immune response in case of a re-infection. • There are over 100 different strains of rhinovirus circulating in the human population!

29. Rhinovirus • Pathology: • Rhinovirus reproduces rapidly, kills relatively few cells in the upper airways (focal infections) and quickly surrenders to the innate immune system. • Therefore, you mainly get symptoms associated with upper respiratory tract inflammation, which produces the “runny nose” that gives the virus its name (rhinos is Greek for nose) • Inflammation also triggers the sneeze reflex that allows the virus to spread. • However, this sneezing can also spread the infection up into the Eustachian tubes and into the sinuses, causing middle ear infections and sinusitis.

31. LRTI, LRTI LRTI, LRTI LRTI, LRTI: Lower respiratory tract infection

32. Respiratory Syncytial Virus (RSV) • The virus is enveloped (i.e. it has a lipid membrane surrounding its protein capsid and nucleic acid) and possesses a single-stranded RNA genome of negative polarity (i.e. negative-strand RNA genome). • Most frequent cause of lower respiratory tract infection in infants and young children. • Most important viral respiratory cause of pediatric hospitalizations worldwide (125,000 hospitalizations /year). • 450 deaths /year. • No vaccines.

33. Respiratory Syncytial Virus (RSV)

34. Three Problems Every Virus Must Solve Reproduce during its “visit” inside its target cell Spread from one individual to another 3) Evade host defenses

35. 1) Reproduce during its “visit” inside a human cell: Attachment Fusion of membranes and Entry Cellular molecule that serves as virus receptor Viral RNA-dependent RNA Polymerase Viral RNA-dependent RNA Polymerase vRNA Nucleus of cell vRNA (-) vRNA (-) Genome replication Transcription of viral genes cRNA (+) vRNA (-) AAAA CAP AAAA CAP AAAA CAP Subgenomic RNAs (+) ~10 AAAA CAP Translation vProteins Cytoplasm of cell

36. 1) Reproduce during its “visit” inside a human cell: F G Budding of newly formed viruses Nucleus of cell Golgi + ER vProteins vRNA (-) genomic Cytoplasm of cell

37. 1) Reproduce during its “visit” inside a human cell: Nucleus of cell F: fusion protein Nucleus of cell Syncytia (Multinucleated Giant Cells) Nucleus of cell

39. Respiratory Syncytial Virus (RSV) 2) Spread from one individual to another: • The virus spreads mainly by respiratory secretions, usually by contamination of hands or fomites such as bedding. • During epidemic periods, spread within hospitals, creches, and day nurseries (nosocomial infections) are common. • Because of the structure of its envelope proteins, RSV is most infectious at normal body temperature • Favorite temperature for the virus: 98.6o F, • which just happens to be similar to that of the lower airways • RSV causes only acute infections except in immunocompromised patients, who may present persistent infections

40. Respiratory Syncytial Virus (RSV) 3) Evade host defenses: • In part, it is what INFANT is studying • RSV infection is detected by TLR4 binding to the F protein, but glycoprotein G appears to downregulate TLR4-mediated signaling, thereby suppressing inflammation. • In addition to TLR4, several other receptors like TLR3, TLR7, and CARD-helicases (RIG-1 and MAVS) detect viral RNA • Production of interferons in RSV-infected cells is not very efficient due to the inhibitory actions of non-structural viral proteins.

41. Respiratory Syncytial Virus Pathogenesis • Illness often starts as a common cold, but in babies, this could rapidly progress to cyanosis and respiratory distress • Typically, there is bronchiolitis, with or without involvement of the lung parenchyma causing pneumonitis. • There is some evidence that RSV infection in infancy may cause long-term respiratory problems • Severe illness carries a significant risk of death at both extremes of age. Cyanosis is a blue coloration of the skin and mucous membranes due to the presence of deoxygenated hemoglobin in blood vessels near the skin surface. It occurs when the oxygen saturation of arterial blood falls below 85-90% (1.5g/dl deoxyhemoglobin). Bronchiolitis is inflammation of the bronchioles, the smallest air passages of the lungs. Pneumonitis is a general term that refers to inflammation of lung tissue. Pneumonia is one type of pneumonitis caused by an infection. Atelectasis is the collapse of part or all of a lung. It is caused by a blockage of the air passages (bronchus or bronchioles)

42. Respiratory Syncytial Virus Pathogenesis YOU CAN WATCH THIS MOVIE HERE: https://www.youtube.com/watch?v=QkxB3cpNjwc Movie?