MCB100 INTRODUCTORY MICROBIOLOGY Spring 2019 Viruses Reading Assignment: Chapter 13

1. MCB100 INTRODUCTORY MICROBIOLOGYSpring 2019 Viruses Reading Assignment: Chapter 13 - Lytic vs. Lysogenic (Latent) Lifestyle – Bacteriophage l - Life cycle of a + strand RNA virus: polio virus - Life cycle of a retrovirus: HIV - Some significant Human Viral Diseases

2. LON-CAPA in MCB100 Homework Set 9 is due: Friday, April 26 at 11 PM (read chapter 14) Homework Set 10 is due: Wednesday, May 1 at 11 PM (read chapters 15 and 16) Homework Set XI “make-up” due: Wed. May 1, 11 PM Extra Credit Set – 3 due: Wed. May 1, 11 PM The make-up homework set (XI), is not “extra credit”. There are 10 regular homework sets and the make –up folder. Each set is worth up to 10 points. Of these 11 homework folders, I drop your lowest score. If you missed a homework set, you should definitely do the“make-up” set. If you got 10s on all 10 regular homework sets you can’t gain more points by doing the “make-up” set, but it’s okay to do the problems for practice.

3. MCB100 Final Exam Monday, 5/6/19 8:00 – 11:00 AM Last name A - N: Room 112 Gregory Hall Last name O – Z: Room 149 NSRC Conflict Exam IF you have a legitimate excuse, contact Dr. Chapman to sign up. Friday, 5/3 at 8:00 – 11:00 AM Monday 5/6 at 1:30 – 4:30 PM or 7 - 10 PM Tuesday, 5/7 at 8:00 – 11:00 AM in Room 242 Burrill Hall

4. Human and Animal Viruses Some human viruses are always in a lyticcycle. These viruses kill human cells. Examples include: Rhinoviruses – small RNA viruses that cause the common cold Enteroviruses – small RNA viruses that cause viral diarrhea (includes polio!) Hepatitis A – an RNA virus that attacks liver cells Hemorrhagic fever viruses, such as Yellow Fever and Ebola virus Some viruses may become latent (dormant) within human cells. These viruses have a stage in their life cycle that includes a DNA copy of their genome. They may disrupt the regulation of cell division and possibly cause cancer. Examples include: Retroviruses – RNA viruses that replicate via DNA intermediates Human Immunodeficiency Virus (HIV) (causes AIDS) Some DNA viruses – Herpes viruses, Chickenpox, Hepatitis B

5. Exiting the old host cell by lysis. Some animal viruses exit a host cell by lysis. These viruses generally do not have an envelope.

6. Exiting the old host cell by budding. Some animal viruses exit a host cell by budding. Unlike lysis, budding doesn’t necessarily kill the host cell. The viral envelope is derived from the cytoplasmic membrane of the old host cell, with some viral proteins embedded within it. Viral glycoproteins mark an infected cell with foreign antigens.

7. An Example of a Human Virus that exits a host cell by lysis Polio Virus - Classified in the Picornaviridae family - non-enveloped, + strand RNA virus - enterovirus (entero = intestines) - Life cycle is similar to the T4 lytic cycle The Life Cycle of the Polio Virus 1. Host Encounters the Pathogen 2. Attachment to host cell 3. Entry into host cell 4. Synthesis of viral components, mRNA, proteins, genome 5. Assembly of new virus particles 6. Release from the old cell

8. Steps in a Viral Infection 1. Host Encounters the Pathogen(fecal – oral cycle) The virus is ingested in contaminated water, or food, or otherwise enters the mouth. 2. Attachment The primary tissue tropism for polio is intestinal epithelial cells. Virus coat proteins stick to receptors on the surface of the host cell. 3. Entry Host cell cytoplasmic membrane encircles the virus enclosing it within a vesicle. Viral capsid breaks open depositing viral genomic RNA into the cytoplasm.

10. 4. Synthesis(occurs totally in the cytoplasm of the infected cell) - Viral genomic RNA is translated by host ribosomes, making viral proteins. (the genomic RNA is + strand, sense) - The viral RNA-dependent RNA polymerase in the cytoplasm copies virus RNA. - A negative sense copy of the viral RNA is made. - The – sense strand of viral RNA is used as a template by the viral RNA polymerase to make new copies of the viral + strand RNA. (for both mRNA and genomic RNA) 5. Assembly - Viral coat proteins spontaneously associate with viral + strand RNA. 6. Release(the host cell is killed – virus exit by lysis of host cell) - When the cell is full of virus particles it breaks open. New virus particles infect other cells within the host or are excreted in feces.

11. Polio Virus Life Cycle Polio is a fecal-oral cycle pathogen. Most cases show mild symptoms. Even in very mild cases an infected host sheds virus particles. The oral polio vaccine is a live, but attenuated or weakened, virus.

12. Polio – The Cause of Disease The death of infected cells is the root cause of disease. The symptoms of the primary infection are minor, possible diarrhea. Neurological symptoms that include paralysis develop when the virus is present in the body in high levels and secondary tissues are attacked. The virus prefers to attack intestinal epithelial cells but may invade nerve cells as a secondary tissue tropism. Death of nerve cells can lead to a loss of muscle coordination and paralysis. Only a small fraction of infections lead to paralytic disease. (Picornaviridiae = small RNA viruses)

14. Viruses 3 - Polio Which ONE of the following statements about polio or the poliovirus is FALSE? A. All cases of infection by the poliovirus lead to paralysis of some muscle groups. B. Polio is an example of a viral fecal-oral cycle disease. C. The primary tissue tropism for the poliovirus is intestinal epithelial cells. D. The replication of poliovirus genetic material requires a virus-specific RNA-dependent RNA-polymerase. E. Poliovirus particles exit an old host cell by causing the cell to lyse (break open).

15. Viruses 3 - Polio Which ONE of the following statements about polio or the poliovirus is FALSE? A. All cases of infection by the poliovirus lead to paralysis of some muscle groups. False. Actuallyparalysis symptoms are seen in about 1% of polio virus infections. Mild diarrhea is common. B. Polio is an example of a viral fecal-oral cycle disease. C. The primary tissue tropism for the poliovirus is intestinal epithelial cells. D. The replication of poliovirus genetic material requires a virus-specific RNA-dependent RNA-polymerase. E. Poliovirus particles exit an old host cell by causing the cell to lyse (break open).

17. HIV (Human Immunodeficiency Virus) HIV is a retrovirus. The viral genomic material is + sense RNA but during replication a double-stranded DNA copy of the genome is made by a viral enzyme called “reverse transcriptase”. Life Cycle of HIV ATTACHMENT - HIV Infects a type of white blood cell known as a T-helper cell. - The viral receptor is a protein called CD4. - CD4 is involved in cell-cell recognition of various types of immune system cells. - T-helper cells assist in communication between various types of immune cells. - T-helper cells play a critical role in coordinating the immune response. Death of T-helper cells shuts down host immunity. ENTRY - Virus envelope fuses with the host cell cytoplasmic membrane. Richard Hunt University of South Carolina School of Medicine

18. a. virus attaches to CD4 protein on surface of a Th-lymphocyte b. viral envelope fuses with cell membrane, capsid enters host cell cytoplasm c. capsid proteins break down releasing viral RNA and reverse transcriptase d. viral reverse transcriptase makes a single-stranded DNA copy of the HIV RNA e. reverse transcriptase reads viral ssDNA to make the complimentary DNA strand f. viral dsDNA enters nucleus and becomes integrated into a host cell chromosome g. host cell RNA polymerase makes viral mRNA h. viral mRNA is translated to make viral proteins (i) j. viral genomic RNA exits nucleus (k) l. viral proteins bind to HIV genomic RNA to make capsids m. HIV envelope proteins (gp41, gp120) are inserted into the cytoplasmic membrane capsids attach to viral proteins in the cell membrane cytoplasmic membrane bends to surround the capsid a new viral particle exits the host cell by budding

19. The envelope, shown in gray, is a lipid bi-layer that is derived from the cytoplasmic membrane of the old host cell. The envelope proteins, colored green and purple, are involved in helping the viral particle to attach to and enter a new host cell. The capsid, blue, is made of proteins that surround the viral RNA. In this picture, viral RNA is colored golden-brown. The red dots represent the viral enzyme, reverse transcriptase, which can make a DNA copy using viral RNA as the template.

21. SYNTHESIS - Viral RNA is read by the viral reverse transcriptase to make a ss DNA copy. - Viral ss DNA is converted to ds DNA by reverse transcriptase. - Viral DNA enters nucleus and is integrated into host chromosome. - Host RNA polymerase transcribes viral DNA sequences to make viral mRNA. - Viral proteins are made in the cytoplasm by host cell ribosomes. - The viral mRNA can act as viral genomic material. ASSEMBLY - Virion particle must contain viral reverse transcriptase enzyme. - Spontaneous assembly of capsid. - Spike proteins embedded in host cell membrane. RELEASE - New virus particles exit the cell by budding.

22. Viruses 4 - Polio virus vs. HIV Which ONE of the following statements about poliovirus and HIV is TRUE? A. Both poliovirus and HIV are most often transmitted by insect bites. B. Both poliovirus and HIV have RNA genomes. C. Both poliovirus and HIV have a life cycle that involves a DNA intermediate stage. D. Both poliovirus and HIV damage the host by killing nerve cells and causing paralysis. E. Both poliovirus and HIV primarily infect a type of white blood cell called CD4 T-helper cells.

23. Viruses 4 - Polio virus vs. HIV Which ONE of the following statements about poliovirus and HIV is TRUE? A. Both poliovirus and HIV are most often transmitted by insect bites. Polio: fecal-oral cycle, HIV: STD B. Both poliovirus and HIV have RNA genomes. C. Both poliovirus and HIV have a life cycle that involves a DNA intermediate stage. HIV: yes, polio: no D. Both poliovirus and HIV damage the host by killing nerve cells and causing paralysis. HIV: no, polio: yes E. Both poliovirus and HIV primarily infect a type of white blood cell called CD4 T-helper cells.HIV: yes, polio: no

24. HIV Infections Prevalence vs. Number of Cases Prevalence gives the rate ofinfection as a fraction of thepopulation. Prevalence iscommonly expressed in unitsof: cases/100,000 or in someinstances, %. (1% = 1/100) Total number of cases inarbitrary geographicalregions does not informthe reader of prevalence.Example: HIV cases in IL and PRare very similar, but thepopulation of IL is 4x thatof PR. HIV prevalence inPR is ~4x as high as IL.

25. The Baltimore Classification Scheme for VirusesViruses are divided into groups on the basis of the type of their genetic material and how they make virus specific mRNAs. Basis: All viruses consist of some nucleic acid, either DNA or RNA, which is the genetic material and a coat or capsid that is made of protein. For an infected cell to make virus specific coat proteins, virus specific mRNAs must be made at some time during the life cycle of the virus. Seven Groups of Animal Viruses I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses) II: ssDNA viruses (+)sense DNA (e.g. Parvoviruses) III: dsRNA viruses (e.g. Reoviruses) IV: (+)ssRNA viruses (+)sense RNA (e.g. Picornaviruses, Togaviruses) V: (−)ssRNA viruses (−)sense RNA (e.g. Orthomyxoviruses, Rhabdoviruses) VI: ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle (e.g. Retroviruses) VII: dsDNA-RT viruses (e.g. Hepadnaviruses)

26. Virus Classification by the Baltimore Scheme transcription by host cell DNA-dependent RNA polymerase virus encoded RNA-dependent RNA polymerase virus encoded RNA-dependent RNA polymerase reverse transcriptasean RNA-dependent DNA polymerase

27. There will be a matching section about viruses that will include several of the following: Polio, Hepatitis B, Chickenpox, HIV, Rotovirus, Rhinoviruses Influenza, Hepatitis A, Rubella, Rubeola, HPV – 16, HSV-2, Ebola Rabies Bacteriophage lambda

28. Examples of Human and Animal DNA Viruses Herpes viruses - includes: HSV1, HSV2, Chicken pox, and EBV Papillomavirus - includes: many strains of HPV, that cause warts Poxviridae - includes: smallpox and cowpox (vaccinia) Parvovirus - includes: Canine parvovirus and Porcine parvovirus Examples of Human DNA Viruses Virus Genome Virion or Disease Nature Size bp Shape Size nm Smallpox ds, linear 200,000 brick, enveloped 250 Herpes Simplex ds, linear 200,000 icosahedral, enveloped 110 Hepatitis B ds, circular 3000 spherical, enveloped 42 Also: Epstein-Barr Virus (EBV), Papilloma viruses (HPV = human papilloma virus)

29. RNA Viruses • Togavirus – example: yellow fever • Rhabdovirus – example: rabies • Paramyxovirus – example: mumps • Orthomyxovirus – example: influenza • Rhinovirus – example: common cold • Enterovirus – example: polio • Retrovirus- example: HIV

30. Examples of Human RNA Viruses Virus Genome Virion or Disease Nature Size bases Shape Size nm Influenza ss, -, segmented 17,000 spherical, enveloped 100 HIV ss, +, retrovirus 8,000 spherical, enveloped 95 Rhinovirus ss, + 6,000 icosahedral, naked 30 Rubella ss, + 14,000 icosahedral, enveloped 45Also: Hepatitis A, Polio virus, Eastern Equine Encephalitis, Ebola, Hanta Virus, Rabies

31. Viruses 5 – DNA viruses and RNA virusesWhich one of the following statements about DNA viruses and RNA viruses is INCORRECT? A. RNA viruses are more likely to cause cancer than DNA viruses. B. In the life cycle of some, but not all, DNA viruses the viral genetic material must get into the host cell nucleus in order to be replicated. C. The replication of the genetic material of an RNA virus like polio involves a virus specific enzyme called an RNA-dependent RNA polymerase. D. The replication of the genetic material of a retrovirus like HIV involves a virus specific enzyme called reverse transcriptase. E. Antibiotics such as penicillin or tetracycline or erythromycin won’t stop a viral infection.

32. Viruses 5 – DNA viruses and RNA virusesWhich one of the following statements about DNA viruses and RNA viruses is INCORRECT? A. RNA viruses are more likely to cause cancer than DNA viruses. B. In the life cycle of some, but not all, DNA viruses the viral genetic material must get into the host cell nucleus in order to be replicated. C. The replication of the genetic material of an RNA virus like polio involves a virus specific enzyme called an RNA-dependent RNA polymerase. D. The replication of the genetic material of a retrovirus like HIV involves a virus specific enzyme called reverse transcriptase. E. Antibiotics such as penicillin or tetracycline or erythromycin won’t stop a viral infection.

33. Influenza is an enveloped virus with a segmented RNA genome. There are two major antigenic spike proteins in the envelope. Hemagglutinin, or H-antigen, is involved in the binding of the virus to a human host cell by attaching to sialic acid residues on cell surface glycoproteins. Neuraminidase, or N-antigen, is an enzyme that cleaves the sialic acid residues off of the host cell surface glycoproteins. This allows new virus particles to be released from the infected cell by budding. Flu symptoms are caused by cell death due to the immune system attacking the infected cells. Damage to the mucosal epithelial tissue makes the host more susceptible to secondary bacterial infection.

34. Left New flustrains canarise byrecombinationbetweenhuman,bird andswinestrains ofthe virus. Above from: www.myhousecallmd.com Below: Flu WardFt. Riley KS - 1917

35. Rubeola vs. RubellaRubeola = Measles Rubella = German Measles Measles is causes by a virus in the family Paramyxoviridiae negative-sense, single-stranded RNA virus enveloped, helical nucleocapsid Transmission: airborne Symptoms: - fever up to 40oC (104oF), cough, runny nose, conjunctivitis - rash of small raised red spots on skin - bright red spots with bluish-white centers in mouth (Koplik’s spots) fatality rates: 0.1% in healthy individuals in developed countries 10% in malnourished children in less-developed countries 30% in immunocompromised individuals German Measles virus is in the family Togoviridiae positive-sense, single-stranded RNA viruse enveloped, icosahedral nucleocapsid Transmission: airborne Symptoms: - mild fever - rash of small red spots that are not raised congenital rubella syndrome in the first trimester of pregnancy can lead to fetal death, premature delivery or a wide variety of congenital defects

36. Hepatitis A vs. Hepatitis B Hepatitis is an inflammation of the liver. Several agents can cause hepatitis. Hepatitis A is in Picornaviridae family, nonenveloped, icosahedral capsid, positive-sense, single-stranded RNA genome, transmitted by fecal-oral cycle, jaundice is common, mortality is < 1% most cases resolve in 4 – 6 weeks Hepatitis B is in the family Hepadnaviridae enveloped, icosahedral capsid, double-stranded, circular DNA genome, transmitted through blood transfusions, shared hypodermic needles, and other bodily secretions, Hepatitis B infects about 300,000 Americans each year and 5000 die from HBV related cirrhosis while 1000 die from HBV related liver cancer.

37. More Examples of Human VirusesDNA Viruses Epstein-Barr Virus (in the family, Herpesviridae) causes infectious mononucleosis and Burkitt’s lymphomaHPV (Human Papilloma Viruses) (family: Papovaviridae) many strains, cause warts (genital warts), attacks growing cells RNA VirusesRabies- Rhabdoviridae - infects CNS - long incubation Ebola- hemorrhagic fever, often fatal - Filoviridiae, natural host? Yellow Fever- hemorrhagic fever- mosquito borne,

38. Papillomaviruses - The human papillomaviruses (HPV) are responsible for producing benign warts. - There are about 100 types of HPV, in the genus Papovaviridae. - Papillomaviruses are naked dsDNA viruses with icosahedral virions composed of 72 capsomeres, 52-55 nm in diameter. - Papillomaviruses have been linked with genital cancers and may be discussed again in unit C-13.

40. Herpes Viruses - dsDNA viruses - many are neurotropic and neuroinvasive and can become latent in the body of nerve cells Herpes Simplex Virus – 1 - causes cold sores and fever blisters (primarily oral) (Lesions are called “herpetic whitlow”.) Herpes Simplex Virus - 2 - HSV2 causes genital herpes - HSV2 was thought to be linked to cervical cancer in the 1960s and 1970s. Now it is thought that cervical cancer is are caused by HPV not HSV. (HSV & HPV are in totally different virus families. Human Papilloma Viruses cause warts.) Varicella zoster (AKA: Herpes zoster) Chickenpox Chickenpox virus can become latent in the dorsal root ganglia, reactivation of the virus causes “shingles”.

41. MIMIVIRUS Example: Acanthamoeba polyphaga mimivirus (APMV) APMV has the largest diameter of all known viruses and a large genome too. APMV was discovered in 1992 within the amoeba Acanthamoeba polyphaga. The virus was observed in a Gram stain and mistakenly thought to be a Gram-positive bacterium. In 2003, researchers in France identified the microorganism as a virus. Mimivirus may be a causative agent of some forms of pneumonia. Mimivirus is the largest known virus, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface of the capsid, bringing the total length of the virus up to 600 nm. It does not appear to possess an outer viral envelope. The mimivirus genome is a linear, double-stranded molecule of DNA roughly 1.2 million base pairs in length.

42. Viral Infections of the Skin - Herpes Simplex Virus - 1 - Chickenpox - Measles - German measles - Warts

43. Herpes Simplex Virus – 1 aka:HSV-1 The Herpes virus HPV-2 will be covered more in later slides which cover urogenital infections. HSV – 1 is the causative agent of oral cold sores and fever blisters. Transmitted by close contact. HSV – 1 is a dsDNA virusthat can become latent in the trigeminal and brachial ganglia. Lateractivation can cause coldsores or fever blisters.

44. Oral Herpes Lesions

45. Chicken Pox varicella zoster virus(in the Herpesvirus family) Portal of Entry: Inhalation Primary tissue tropism: respiratory epithelial tissues Secondary Tissue tropisms: viruses spread through blood and lymph (viremia) and infect liver, spleen and lymph nodes, and later: skin and nerve ganglia.Viruses are shed through respiratory droplets and from the skin lesions. Viruses can become latent in the nerve ganglia.

46. Shingles are a later manifestation of chickenpox.

47. Measles aka: red measlesaka: rubeola Rubeola is one of the more contagious and serious of childhood diseases and should not be confused with the generally milder infection, rubella (German measles). Portal of Entry:Respiratory Tract Lethality: varies withthe health of the host

48. Measles can be diagnosed by the presence of Koplic’s spots in the mouth. These spots are red with a bluish-white center.

49. Rubella, aka: German Measles, is milder than rubeola. The red spots are not raised and Koplic’s spots are not seen. Rubella virus can cross the placenta and cause birth defects in a developing fetus.

50. Seed warts