1. Virology Review Alyson Yee Medical Microbiology 4/11/16

2. Exam format & hints Short answer Approximately 50/50 mix of basic biology and clinical (case studies) Lectures (slides, notes, recordings) are high yield Questions worth multiple points require you to state multiple facts Practice exam on Chalk under Reviews

3. Things to know About each bug: Virus classification (genome type, envelope) Mode of transmission Basic clinical picture What makes this bug unique? What about the biology helps explain the associated disease? About treatment/prevention: Be able to read the serology charts for HIV, Hep B Know specific vaccines discussed in lecture

4. Virus Structure: the virion Stability of the virion affects mode of transmission. Naked capsids are generally more stable outside the human body.

5. Viral genetics Adapted from Medical Micro Made Ridiculously Simple dsDNAmRNA Viral gene products ssDNA dsDNA mRNA Viral gene products + RNA Viral gene products - RNA+ RNAViral gene products DNA viruses RNA viruses RNA DNA mRNA Viral gene products Retroviruses: Reverse Transcriptase Viral RNA-dependent RNA polymerase

6. Generic viral life cycle

7. Viral size A key theme is genetic economy Capsids are usually symmetrical because they are constructed from 1 or a few identical protein subunits Size of capsid is proportional to size of genome Small viruses (ex parvovirus-3) have “Swiss Army Knife” genes Big viruses (ex Poxvirus-250)

8. Host defenses against viruses PRIMARY: Physical and chemical barriers (skin, acids and inhibitors made by commensal microbiota) IMMUNE: Innate (NK cells, TLRs recognize general viral components like structures in the wrong compartment, uncapped mRNA, etc and trigger interferons to activate T cells Adaptive (B cells and cytotoxic T cells)

9. Factors influencing viral disease Primary tissue infected Mode of transmission Cell-specific receptor expression Effects on host Cytopathic Cellular transformation Spread of virus/secondary sites of infection Immune response

10. Viral evolution 1.Generation of point mutations - many viral polymerases (esp. RNA polymerases) have poor fidelity. Lack proofreading. - rapid viral life cycle and large burst size create accelerated evolution 2.Genetic re-arrangements -recombination between similar viruses -influenza: reassortment Major obstacle in viral therapeutics: - Drug resistance - Resistance to immune response - Ineffective vaccination

11. Acute vs. Persistent Infection

12. DNA viruses

13. Naked DNA viruses Stable in hostile environments Released by lysis Need neutralizing mucosal and systemic antibodies to prevent infection

14. Human Papillomavirus (HPV) TYPE: non-enveloped dsDNA TRANSMISSION: sexual (some types) CLINICAL: warts; high risk types lead to cervical, ano- genital, head and neck cancers Infect basal cell layer and as epithelium differentiates, later genes expressed to produce more virions, so only the upper layers contain infectious particles UNIQUE: Push the cell into S phase to use host replication machinery. Can cause oncogenic transformation in non- permissive cells. E6= transforming protein that degrades p53 E7 = transforming protein that binds & inactivates Rb

15. Human Papillomavirus (HPV) DIAGNOSIS: cytology (Pap smear—look for koilocytes) TREATMENT: remove warts, treat w/ interferon PREVENTION: subunit vaccine against L1 (capsid) has been available since 2006. Tetravalent vaccine is against 16, 18, 6, 11. Recommended for both males and females before sexual activity. Protects against 70% of cervical cancers - other high risk strains, such as 31 & 45 are not in vaccine. halo NormalKoilocyte binucleate

16. Polyomavirus: BK and JC TYPE: non-enveloped dsDNA TRANSMISSION: aerosol, ubiquitous CLINICAL: usually asymptomatic unless immunocompromised. BK: kidney JC: lytic infection of oligodendrocytes leading to demyelinating disease (PML) with sensory and motor loss, cognitive impairment UNIQUE: establish persistent and latent infections. Can spread through blood (viremia). New polyomaviruses (Merkel Cell polyoma, KI, WU isolated from sequencing so unknown if they are infectious or benign) DIAGNOSIS: BK: virus can be detected in urine. JC: histology, MRI/CT, brain biopsy

17. Adenovirus TYPE: non-enveloped dsDNA TRANSMISSION: aerosol, fecal-oral depending on strain CLINICAL: Direct cell damage in mucoepithelial cells, persists in lymphoid tissue by infecting migrating DCs. UNIQUE: Disease depends on tissue tropism: usually eye (conjunctivitis), upper respiratory (pharyngitis without fever). Fiber projecting from capsid enables attachment, hemagglutination, cytotoxicity DIAGNOSIS: viral culture, PCR TREATMENT: none PREVENTION: live oral vaccine for military

18. Parvovirus (B19) TYPE: non-enveloped ssDNA (either + or – can be packaged) TRANSMISSION: aerosol CLINICAL: Initially infects upper respiratory tract, leads to viremia. Major cell type for replication is erythroid precursors in bone marrow/fetal liver. Causes Fifth’s disease (slapped cheeks), aplasia, hydrops fetalis UNIQUE: ssDNA, can arrest RBC production so dangerous for sickle cell patients DIAGNOSIS: B19: ELISA for B19-specific IgM and IgG, hydrops: by ultrasound during pregnancy TREATMENT: immune globulin, intrauterine transfusions

19. Enveloped DNA viruses Herpes Pox

20. Herpesvirus latency Human Herpesviruses Acronym Name Site of latency HSV-1Herpes simplex virus 1 sensory neurons HSV-2 Herpes simplex virus 2 sensory neurons VZV Varicella-Zoster virus sensory neurons CMV Human cytomegalovirus monocytes, endothelial cells HHV-6A T cells, monocytes HHV-6B T cells, monocytes HHV-7 T cells EBV Epstein Barr Virus B lymphocytes HHV-8(Kaposi’s sarcoma Monocytes ? associated virus)

21. Herpes simplex (HSV1 & HSV2) TYPE: enveloped dsDNA TRANSMISSION: direct contact CLINICAL: recurrent oral (usually HSV1) and genital lesions (usually HSV2), complications including encephalitis, keratitis, neonatal herpes UNIQUE: two distinct programs of infection (productive and latent). Carry own polymerase. After primary of infection, virus infects sensory nerve endings, retrograde travel to nucleus, latent infection, reactivates, travels back down axon and infects other cells nearby causing lesion. In latency, only 1 RNA (the LAT) is expressed so antivirals cannot target viral enzymes DIAGNOSIS: Tzanck smear for multinucleated giant cells, DFA TREATMENT: acyclovir (chain terminator; requires active infection because relies on viral thymidine kinase)

22. Natural history of herpes simplex virus 1 Establishment of latency Retrograde transport Disseminated infection of newborn Adult encephalitis No manifestations or.. Anterograde transport Reactivation Recurrent keratitis

23. Varicella Zoster TYPE: enveloped dsDNA TRANSMISSION: respiratory CLINICAL: primary infection causes chickenpox (varicella) in children, reactivates as shingles (zoster) in adults (1 dermatome) and can lead to cranial nerve pain UNIQUE: latent in dorsal root ganglion, reactivation as shingles later in life, generates protective immunity that wanes over time DIAGNOSIS: clinical PREVENTION: Live attenuated vaccine, higher dose for secondary “shingles vaccine” vs. primary “chicken pox vaccine” infection to overcome pre-existing immunity.

24. Cytomegalovirus TYPE: enveloped dsDNA TRANSMISSION: direct contact, transplacental CLINICAL: Congenital: petechiae, jaundice, hepatosplenomegaly, neurologic abnormalities, microcephaly. Immunocompromised: retinitis, pneumonia, etc. UNIQUE: latency in monocytes, virus excreted in saliva and urine DIAGNOSIS: detect virus in blood/saliva/urine. Infected cells have owl eye appearance TREATMENT: gancyclovir (relies on phosphorylation by viral protein kinase)

25. Epstein Barr Virus TYPE: enveloped dsDNA TRANSMISSION: saliva CLINICAL: Infectious mononucleosis: fatigue, malaise, pharyngitis, hepatosplenomegaly. Neurologic: nerve palsy, Guillian-Barré, meningoencephalitis. Thrombocytopenia purpura (low platelets). Malignancies: Burkitt’s lymphoma (lymphadenopathy in central African children), some Hodgkins disease UNIQUE: latency in B lymphocytes, lytic infection in oropharyngeal/salivary cells. Latently infected cells become immortal and contain circular plasmid. DIAGNOSIS: heterophile antibody titers TREATMENT: NSAIDs, acetominophen (not aspirin or you risk Reye’s). Refrain from sports due to hepato- & splenomegaly.

26. Roseola (HHV6 & HHV7) TYPE: enveloped dsDNA TRANSMISSION: saliva (mother to child) CLINICAL: one of the main childhood febrile illnesses UNIQUE: primary infection in first year of life, most adults are HHV6 seropositive

27. Kaposi’s Sarcoma-associated Herpesvirus (HHV8) TYPE: enveloped dsDNA TRANSMISSION: saliva, sexual/blood CLINICAL: etiologic agent of Kaposi’s sarcoma (an AIDS defining illness), can occur in transplant UNIQUE: gamma herpesvirus, endemic in some parts of Africa TREATMENT: remove tumor, irradiation/chemo, HAART therapy in AIDS patients

28. Poxvirus Replication -cytoplasmic life cycle unique for DNA viruses.

29. Poxvirus TYPE: enveloped dsDNA TRANSMISSION: contact CLINICAL: Smallpox: eradicated. Manifested as centrifugal rash. Molluscum contagiosum is spread by direct contact and can resolve or persist if immune compromised UNIQUE: size (huge genome), cytoplasmic life cycle, asymmetric capsid that is hardy even though enveloped. DIAGNOSIS: EM, gel diffusion PREVENTION: vaccine (know the history of variolation/vaccination) TREATMENT: immune globulin

30. RNA viruses

31. ss (+) RNA viruses (+) strand RNA genome can be directly translated upon release into cell (immediately infectious) Usually short genomes because RNA dependent RNA polymerase lacks proofreading (exception: Coronaviruses) Usually cytolytic Generally make 1 polyprotein and process later

32. Picornaviruses PERCH: Divided into enteroviruses (Polio, Echovirus, Cocksackie A & B) and Rhinoviruses (and Hepatitis A) Enteroviruses are nonenveloped and resistant to environment (fecal-oral route) Rhinoviruses also naked but prefer upper respiratory tract because more sensitive to acid in gut, optimized to 33 o C Disease determine by 1) tissue tropism and 2) cytolytic capacity

33. 1.Entry via the oropharynx, intestinal mucosa or upper respiratory tract 2. Primary infection: lymphatic tissue 3. Spread to the target tissues: EV and HAV spread by viremia 4. Disease factors: (I) target tissues, (II) cytolytic capacity of the virus 5. Virus shedding: (I) feces, EV and HAV, (II) nasal secretion (HRV) Picornavirus Pathogenesis

34. Polio TYPE: nonenveloped ss (+) RNA TRANSMISSION: fecal-oral CLINICAL: causes subclinical disease, minor illnesses, aseptic meningitis, or frank poliomyelitis UNIQUE: Primary viremia and accesses target tissue (brain & meninges)  paralysis PREVENTION: vaccine (know the history of Salk vs. Sabin) TREATMENT: no cure, iron lung

35. Other enteroviruses TYPE: nonenveloped ss (+) RNA TRANSMISSION: fecal-oral CLINICAL: They are all major causes of aseptic meningitis. Cocksackie A causes Hand-foot-mouth disease, herpangina. Cocksackie B causes pericarditis, myocarditis. Echovirus (acroynm) causes acute febrile illness, Guillian-Barré. DIAGNOSIS: serology (specific IgM); isolate virus from throat, stool, CSF; specific antibodies by ELISA or immunofluorescence; PCR PREVENTION: vaccine for polio only TREATMENT: Pleconaril (interacts with capsid and blocks viral entry), Rupintrivir and other viral proteinase inhibitors (block cleavage of polyprotein). But high mutation rates so resistance easily developed, so treat with a cocktail

36. Rhinovirus TYPE: nonenveloped ss (+) RNA TRANSMISSION: aerosol, direct contact CLINICAL: major cause of the common cold. Symptoms are mainly immune-mediated. Virus is shed through nasal secretions UNIQUE: Liable to acid (unable to replicate in GI tract), grows at 33’C so prefers upper respiratory tract PREVENTION: Not a vaccine candidate because >100 serotypes, transient antibody response TREATMENT: nasal vasoconstrictors, some antivirals to inhibit uncoating, RdRP, proteinase

37. Norovirus TYPE: nonenveloped ss (+) RNA TRANSMISSION: fecal oral CLINICAL: acute, self-limiting GI disease (vomiting, diarrhea) UNIQUE: No animal model, only in humans DIAGNOSIS: PCR PREVENTION: No cruises  TREATMENT: oral rehydration

38. Arboviruses Enveloped ss (+) RNA Replicate in cytoplasm Most have arthropod vectors (usually mosquitoes or ticks) Divided into Togaviruses (Chikungunya) and Flaviviruses (Yellow Fever, Dengue, West Nile)

39. Arbovirus: Togavirus: Alphavirus: Chikungunya and EEVs TYPE: Enveloped ss (+) RNA TRANSMISSION: mosquito CLINICAL: debilitating, prolonged joint pain, rash. Infect muscle and lymph nodes at initial site, spread via viremia to distant skeletal muscle or nervous system. Causes encephalomyelitis (WEE, EEE, VEE) UNIQUE: Most alphaviruses are mostly in animals (equine encephalitis viruses but can cause encephalitis in humans) except Chikungunya. Point mutation in viral envelope allowed spread into a different mosquito DIAGNOSIS: PCR, serology PREVENTION: eliminate mosquitoes TREATMENT: killed virus vaccine against encephalitic alphaviruses for high risk populations

40. Toga WEE EEE VEE Western Equine Encephalitis, Eastern EE, Venezuelan EE Diseases: encephalomyelitis, arthritis, rash Primary site  Viremia  Secondary site

41. Flaviviruses: Yellow Fever, West Nile, Dengue, (Zika) TYPE: Enveloped ss (+) RNA TRANSMISSION: mosquito CLINICAL: YFV: mosquito borne hemorrhagic fever (jaundice, hepatitis) with 20-30% fatality. Dengue: “breakbone” fever, hemorrhagic fever, shock. WNV: hemorrhagic fever that can progress to encephalitis UNIQUE: WNV uses avian amplifier hosts and overwinters in a mosquito with unlimited geographic range. Dengue has antibody-dependent enhancement (previous infection with a different serotype increases likelihood of hemorrhagic fever/shock) DIAGNOSIS: PCR, serology PREVENTION: eliminate mosquitoes TREATMENT: live attenuated vaccine against YFV available (17D)

42. Dengue Virus Antibody-dep. Enhancement: Previous infection with with a different Dengue seroptype increases likelihood of developing DHF/DSS The primary target cells of flaviviruses are of monocyte-macrophage lineage. Flavivirus infection is enhanced 200-1000 fold by non-neutralizing antiviral antibodies that promote virus binding to Fc receptors.

43. Stages of West Nile Virus Infection Host Entry By Mosquito Innoculation First round of replication in the skin: Langerhans dentritic cells (LDC) LDC migrate to draining lymph nodes Secondary round of replication occurs Viremia Viceral Organs CNS Destruction of neurons (Liver, kidney, spleen) ?

44. Rubella TYPE: Enveloped ss (+) RNA TRANSMISSION: respiratory CLINICAL: Respiratory virus  viremia and spreads to other tissues, can cross placenta (problem: congenital infection) UNIQUE: considered a togavirus but not arthropod borne. Non cytolytic, severe teratogenic effects on fetus DIAGNOSIS: clinical, anti-Rubella IgM PREVENTION: part of MMR vaccine TREATMENT: none

45. 1. Genomic RNA cannot function as mRNA 2. Genomic RNA serves as a template for two kinds of RNA: mRNA and complementary, genomic RNA (cRNA) 3. Since cells do not have RNA dependent RNA polymerases, negative strand viruses package the enzyme in the virion All negative strand viruses infecting humans: Are enveloped Enter cells by fusion of envelope with cellular membranes Egress the infected cell by budding Become infectious on egress Are sensitive to lipid solvents, drying, etc. Negative strand viruses: general definition

46. INFLUENZA IS HIGH YIELD.

47. Influenza TYPE: Enveloped ss (-) segmented RNA TRANSMISSION: aerosol CLINICAL: often the culprit in secondary bacterial pneumonia UNIQUE: segmented RNA genome (allows for genetic shift with reassortment), nuclear replication unusual for RNA viruses. Must do cap-stealing to stay stealth. DIAGNOSIS: clinical PREVENTION: seasonal tetravalent vaccine (live attenuated nasal vs. killed shot). Vaccine must be made every year because of genetic drift TREATMENT: Tamiflu/oseltamivir (most flu now resistant), zanamivir. Work by blocking NA. Must give early in infection or prophylactically.

48. Nuclear replication (unusual for RNA viruses) - cap stealing, mRNA splicing Fusion and uncoating Packaging Low pH Influenza virus life cycle

49. Differentiation of Influenza A, B, and C Genetically related: all orthomyxoviruses Influenza A: infect humans, poultry, pigs, etc., wild aquatic birds are usually the natural host re-assort most virulent associated with pandemics Influenza B: predominantly infects humans (and seals) less virulent and less common than A No reassortment so far Seasonal epidemics Co-circulates with A virus Influenza C: humans, dogs and pigs least common Seasonal Tetravalent Vaccine: A – H1N1 A – H3N2 B – Yamagata-lineage B – Victoria-lineage

50. Orthomyxoviruses: Antigenic Drift vs. Antigenic Shift Antigenic Drift = Minor mutations in NA and HA that make our immune response less effective Antigenic Shift = two influenzas in one cell undergo reassortment and now there’s a new combination of HA and NA. Pandemics caused by shift

51. Paramyxoviridae Measles Mumps RSV Parainfluenza Commonality: Cell-cell fusion (multinucleated giant cells)

52. Measles TYPE: Enveloped ss (-) RNA TRANSMISSION: super contagious. Usually through coughing or sneezing but can live in airspace/on doorknobs for a few hours CLINICAL: Rash, fever, conjunctivitis, inflammation and cough, Koplik’s spots in cheek. Rare outcomes: postinfectious encephalitis, subacute sclerosing panencephalitis UNIQUE: form syncytia to spread between cells without being subject to humoral immunity PREVENTION: part of MMR vaccine (live attenuated— needs T cell immunity) TREATMENT: Vitamin A, immune globulin

53. Mumps TYPE: Enveloped ss (-) RNA TRANSMISSION: aerosol, contact CLINICAL: Tropism for glands: causes parotitis, orchitis, etc. Used to be a major cause of viral meningitis, deafness in children. UNIQUE: form syncytia to spread between cells without being subject to humoral immunity PREVENTION: part of MMR vaccine (live attenuated— needs T cell immunity) TREATMENT: experimentally with interferon

54. Respiratory Syncytial Virus (RSV) TYPE: Enveloped ss (-) RNA TRANSMISSION: aerosol CLINICAL: causes respiratory illnesses from cold to pneumonia and bronchiolitis, especially in infants. Most common cause of hospitalization of kids. Natural immunity doesn’t prevent reinfection (reduced severity) UNIQUE: form syncytia (requires F protein for fusion) to spread between cells TREATMENT: supportive care, ribavirin, passive immune prophylaxis against F protein

55. Parainfluenza Virus TYPE: Enveloped ss (-) RNA TRANSMISSION: aerosol, direct contact CLINICAL: infection localized to respiratory tract, second to RSV in severe pediatric respiratory disease. Natural immunity doesn’t prevent reinfection. UNIQUE: form syncytia (requires F protein for fusion) to spread between cells TREATMENT: immune prophylaxis and ribavirin not effective for hPIV. Large doses of corticosteroids may shorten duration of intubation.

56. Rhabdovirus (Rabies) TYPE: Enveloped ss (-) RNA TRANSMISSION: animal bite CLINICAL: pain at site of bite, flu-like symptoms, cerebral dysfunction, confusion, delirium, etc. (hydro/photo/aerophobia). Fatal if untreated. UNIQUE: rod/bullet shaped capsid. Slow replication/long lag time so post-exposure prophylaxis effective. Travels retrograde to DRG/spinal cord and neurodegeneration occurs DIAGNOSIS: histology: Negri bodies in neurons TREATMENT: immediate post-exposure prophylaxis.

57. Reovirus (Rotavirus) TYPE: Nonenveloped (double capsid) segmented dsRNA TRANSMISSION: fecal-oral CLINICAL: severe gastroenteritis and dehydrating diarrhea in children UNIQUE: double capsid and dsRNA. To hide the dsRNA, remains inside inner capsid until after transcription. Transcription occurs at vertices of capsid. Core viral enzymes cap and methylate mRNAs. PREVENTION: vaccine created by genetic reassortment TREATMENT: rehydration

58. Retroviruses HIV HTLV

59. HIV TYPE: Retrovirus (2 identical + ssRNA) TRANSMISSION: sexual, bloodborne CLINICAL: Acute: mononucleosis-like symtpoms that subside quickly. Latency, immune suppression leading to opportunistic infections (AIDS) UNIQUE: reverse transcription to make DNA from RNA (RT very error prone), obligate integration into chromosomal DNA. Virus must bind to 2 receptors: CD4 and a coreceptor. The coreceptor determines tropism. DIAGNOSIS: PREVENTION: condoms and prophylactic HAART TREATMENT: Highly aggressive anti-retroviral therapy

60. HIV life cycle

61. In addition to CD4, a CORECEPTOR is needed. M-tropic strains use the chemokine receptors CCR5 T-tropic strains use the chemokine receptor CXCR4 CCR5CXCR4 CCR5 - associated with virus transmission CORECEPTOR SWITCH CXCR4 - associated with disease progression

62. AIDS = HIV + … CD4 <200 cell/uL Or one of AIDS-defining illnesses: Respiratory/oral candidiasis Coccidiomycosis Cryptococcus (meningitis) Cryptosporidiosis CMV encephalopathy/colitis Histoplasmosis, disseminated Kaposi’s sarcoma Mycobacterium avi complexa Pneumocystis carinii pneumonia PML (JC virus) Toxoplasmosis Etc (LOTS OF OTHERS)

63. HIV antivirals Latent reservoir Due to integration, virus persists and is never cleared Can’t eradicate HIV once infected HIV = moving target High replication rate High mutation rate (no proofreading) Can quickly develop resistance Reverse transcriptase inhibitors RT is a virus specific enzyme critical for replication Nucleoside RTIs Chain termination Competitive inhibition Non-nucleoside RTIs Used in triple therapy Act by competitive inhibition

64. Vaccines? Despite significant research & $$$, minimal progress towards successful vaccine development Problems: What are the correlates of immunity? -Patients do not clear infection, so no immune correlates are known -Virus can spread from cell to cell, so a live attenuated vaccine is likely more efficacious, but safety concerns due to integration into human chromosomes Possibilities: long-term non-progressors & elite controllers (>1% of HIV-infected individuals) “control” infection & do not progress to AIDS – How?

65. Human T cell leukemia virus TYPE: Retrovirus (2 identical + ssRNA) TRANSMISSION: sexual, bloodborne CLINICAL: immortalizes T cell, oncogenic UNIQUE: tax gene can activate cellular genes to sustain lymphocyte growth HTLV1 = isolated from adult T cell leukemia HTLV2 = isolated from hairy cell leukemia

66. Reminders Do the practice exam! Let me know if you have questions (ayee@uchicago.edu) Lecture material will be highest yield Think about the take home message for each virus Think in clinical cases

67. Hepatitis Hepatitis A Hepatitis E Hepatitis C Hepatitis B = Hepadnaviruses DNA viruses Hepatitis D

68. Viral Hepatitis Etiologic Agents Viruses that specifically target the liver: Hepatitis A, B, C, D, E, G viruses Viruses that sporadically cause hepatitis: Yellow fever virus (a flavivirus) Rubella virus (a togavirus) Enteroviruses (picornaviruses) Cytomegalovirus (a herpesvirus) Herpes simplex virus (a herpesvirus) Epstein-Barr virus (a herpesvirus)

69. Hepatitis Viruses Similarities: infect and damage the liver, causing classic symptoms of jaundice and liver enzyme release usually are not cytolytic pathology is likely due to the immune response difficult to propagate in cultured cells Differences : - structure - genetic material and mode of replication - transmission - the course and the outcome of the disease

70. Viral Hepatitis Overview Source of virus Route of transmission Chronic infection Prevention modification fecesblood/ blood-derived body fluids blood/ blood-derived body fluids blood/ blood-derived body fluids feces fecal-oralpercutaneous permucosal percutaneous permucosal percutaneous permucosal fecal-oral noyes no pre- exposure immunization pre/post- exposure immunization blood donor screening; risk behavior modification pre/post- exposure immunization; risk behavior ensure safe drinking water Types of Viral Hepatitis A BC DE

71. Hepatitis A TYPE: Nonenveloped ss (+) RNA TRANSMISSION: fecal-oral CLINICAL: acute hepatitis, fatigue and fever and abdominal pain followed by jaundice UNIQUE: primary cause of acute hepatitis, picornavirus but grows slowly and not cytolytic DIAGNOSIS: IgG in serum PREVENTION: Inactivated HepA vaccine, immune globulin prophylaxis

72. Hepatitis B TYPE: Hepadnavirus (small, enveloped, circular DNA, behaves like retrovirus) TRANSMISSION: blood borne and sexually CLINICAL: replicates in hepatocytes and can integrate into chromatin. Cell-mediated immune lysis leads to symptoms but can clear infection. Can get hypersensitivity reaction (type III) to immune complexes with Ab and HBsAg. Insufficient T cell response can lead to chronic disease UNIQUE: behaves like a retrovirus DIAGNOSIS: A unique pattern of antibodies in serum. Learn it. PREVENTION: Vaccine: HBsAg-containing pseudovirus particles, passive immunization TREATMENT: antivirals for chronic HBV infection

73. Hepatitis B Virus (HBV) Dane particle (infectious): (1) envelope: hepatitis B surface antigen (HBsAg) (2) the core (HBcAg, HBeAg) (3) circular ds DNA genome in a complex with polymerase. (4) DNA polymerase Other non-infectious forms: The small, spherical HBsAg particle consists of HBsAg with some M. The filamentous fiber has S, M, and L HBsAg forms. Note: HBV contains Reverse Transcriptase

74. Replication of HBV Entry, uncoating Entry into nucleus Completion of dsDNA genome Transcription Cytoplasmic RNAs are: - translated or - reverse-transcribed to form partially dsDNA genome Genome is packaged and released by exocytosis Pseudo-retrovirus???

75. HBV Serologic Diagnosis-learn it! Acute HBVChronic HBV

76. HBV serological diagnosis HBsAgAnti-HBsAbHBeAgAnti-HBeAbAnti-HBcAb Acute HBV + +IgM Window + Chronic HBV (high inf) + +IgG Chronic HBV (low Inf) + +IgG Recovery + +IgG Immunized + Remember: IgG indicates long-term host-exposure to viral particle targeted by antigen IgM indicates short-term host-exposure to target antigen

77. Hepatitis D TYPE: enveloped, ssRNA TRANSMISSION: blood borne and sexually (coinfection or superinfection with HBV) CLINICAL: direct cytopathic effect (40% of fulminant disease) leading to hepatic encephalopathy, necrosis. UNIQUE: requires HBsAg coat for transmission (so piggybacks on Hep B). Uses HBV to produce its 1 protein PREVENTION: see HBV TREATMENT: see HBV

78. Hepatitis C TYPE: enveloped, (+) ssRNA (Flavivirus) TRANSMISSION: blood borne (IV drug use) CLINICAL: cell mediated immunopathology. Promotes development of cirrhosis, PHC, liver failure. Triad of steatosis, bile duct damage, lymphoid follicles in portal tracts. Up to 80% of those exposed progress to persistent infection UNIQUE: Uses 1 polyprotein and chops it up. Antibodies not protective. DIAGNOSIS: look for antibody to HCV antigens, RNA assay TREATMENT: transition from Interferon/ribavirin to antivirals targeting viral proteins: polymerase (nucleoside analog), protease, and NS5A inhibitors in various combinations. >95% cure rate against most HCV genotypes. Expensive!

79. Natural History of HCV Infection Lauer et al. 2001 N Engl J Med 345(1): 41-52. Disease progression risk factors: Sex, age, race, alcohol/drug use, co-infection Chronic HCV is the leading indicator for liver transplant - very slow disease (~30 years)

80. Hepatitis E TYPE: Nonenveloped (+) ssRNA TRANSMISSION: fecal-oral CLINICAL: similar to HAV with high mortality in pregnant women UNIQUE: no chronic infection DIAGNOSIS: enzyme immune assay (anti-HEV IgM) TREATMENT: immune globulin lessens but does not prevent infection

81. A, B, Cs of Viral Hepatitis A –fecal-oral spread: hygiene, drug use, men having sex with men, travelers, day care, food –vaccine-preventable B –sexually transmitted – 100x more infectious than HIV –blood-borne (sex, injection drug use, mother-child, and health care) –vaccine-preventable C –blood borne (injection drug use primarily) – 4-5 times more common than HIV –NOT vaccine-preventable!

82. Why are viruses traditionally difficult to treat? Most bacteria have their own machinery for macromolecular synthesis that are distinct from humans- these can be targeted by antibiotics. Also biochemically distinct cell walls. Viruses use human machinery for macromolecular synthesis (ribosomes, etc.) Difficult to find antiviral targets that are not toxic to humans. Note: viruses are not treatable by broad spectrum antibiotics. Their misuse increases development of drug resistant bacteria. Do not prescribe them for probable viral infections!

83. Viral vaccines Hepatitis A: formalin-inactivated whole virus Hepatitis B: Recombinant HbSAg (covers HDV too) VZV: live, attenuated virus Polio: inactivated (Salk) and attenuated (Sabin) Flu: live attenuated (intranasal) or formalin-inactivated (flu shot) MMR: live attenuated for measles, mumps, rubella HPV: Contains Ag from strains 16 and 18 (Merck also contains 6 and 11 that cause warts) Yellow fever Rabies (post-exposure) Rotavirus (passive immunization with antibodies)

84. Table for antiviral Drug:Viruses: Chemical Type: Target: Acyclovir, VidarabineHerpesviruses (HSV) Nucleoside analogues Virus polymerase GanciclovirCytomegalovirus (CMV) Nucleoside analogue Virus polymerase (needs virus UL98 kinase for activation) Nucleoside-analog reverse transcriptase inhibitors (NRTI): AZT (Zidovudine), ddI (Didanosine), ddc (Zalcitabine), d4T (Stavudine), 3TC (Lamivudine) Retroviruses (HIV) Hepatitis B virus Nucleoside analogue Reverse transcriptase Non-nucleoside reverse transcriptase inhibitors (NNRTI): Nevirapine, Delavridine Retroviruses (HIV) Nucleoside analogue Reverse transcriptase Protease Inhibitors: Saquinavir, Ritonavir, Indinavir, Nelfinavir HIV Peptide analogue HIV protease Ribavirin Broad spectrum: HCV, HSV, measles, mumps, Lassa fever Triazole carboxamide Virus replicase (complex action, direct or indirect) Amantadine / RimantadineInfluenza A strains Tricyclic amine Matrix protein InterferonsHepatitis B and CProteinCell defense proteins activated Zanamavir, OseltamavirInfluenza A and B Substrate analogue Viral neuraminidase Protease Inhibitors: Boceprevir, Telaprivir, Olysio HCVHIV protease

85. Antivirals I: Nucleoside analog prodrugs Requires viral enzyme for activation, so not toxic to non-infected cells Membranes not very permeable to nucleosides, so better to bring them in as prodrug Acyclovir (HSV1&2): Chain terminator Gancyclovir (CMV): Inhibits polymerase Ribavirin (RSV, HCV): Inhibits guanosine synthesis, HIV reverse transcriptase, induces hypermutation Note for acyclovir resistance in immunocompromised patients, use Foscarnet (polymerase inhibitor, not a prodrug)

86. Antivirals II: Flu Block uncoating of Influenza A (bind to M2 ion channel): Amantadine Rimantadine Problems with resistance Neuraminidase inhibitors (block viral release): Oseltamavir (Tamiflu) Zanamavir Must be taken early in infection but useful for high risk contacts

87. Antivirals III: HAART for HIV Nucleoside inhibitors: incorporated into replicating DNA strand, chain termination. Non-nucleoside inhibitors: bind the polymerase and inhibit enzymatic activity. Protease Inhibitors: freq. modified peptide like structures that mimic substrate and irreversibly inhibit protease activity HAART = minimum of 2-3 drugs classes. If this cocktail fails, add: Integrase inhibitors Entry/fusion inhibitors

88. Antivirals IV: Immune molecules Interferons Mainly alpha interferons used for antiviral Activate host immune system Hep C, Hep B, HPV lesions Many adverse side effects, including flu-like symptoms Immune globulins: used for various viruses When a drug ends in “Ab” it’s an antibody