Virology BIOL S02 (Fall 2013) 3pm 6pm COURSE SYLLABUS

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1 Instructor: Peter R. Shank, Ph.D., BMC/GG Rm. 595 Phone: TA: Stephen Zins Phone: Virology BIOL S02 (Fall 2013) 3pm 6pm COURSE SYLLABUS Textbook: Viruses and Human Disease, Strauss, J.H. and Strauss, E.G. 2 nd Ed Academic Press, Washington DC Other sources: Principles of Virology, Flint, S.J., et al. 2 nd Ed ASM Press, Washington DC Fields Virology, Fourth Edition, Eds., Fields, B.N., Knipe, D.M., and P.H. Howley., Lippincott-Raven Publishers, Philadelphia. (This is a two volume version of Fundamental Virology) Viruses, Plagues, and History, Oldstone M.B.A., An excellent review of the triumphs and challenges of virology from a historical perspective. FLU, the Story of the Great Influenza Pandemic of 1918 and the Search for the Virus that Caused It, Kolata, G., An interesting account of the devastation caused by pandemic flu. Course Description: The emphasis of this course will be on understanding the molecular mechanisms of viral pathogenesis. It will begin with a general introduction to the field of virology and then focus on the biology of specific viruses that are associated with human disease. Lectures will be based on the current literature; the text will serve as background material. Grading: Midterm exam (10/16/13) covers lectures 1-6 and is worth 100 points. Final exam (12/18/13): covers primarily lectures 6-12 but includes some material from the first part of the course (150 points). Online problem sets: These will be based on the assigned primary papers. There are a total of 10 and they are worth 10 points each.

2 Lecture Schedule Lecture 1: Introduction, History and Methods 9/4 Composition, Structure and Classification Sep 4, 2013: GRO-Main Campus-Bldg D Chapters 1 and 2 Fouchier et al., Koch s postulates fulfilled for SARS virus. Nature 423:240. Suttle, C.A Viruses in the Sea Nature 437: Raoult, D. et al., The Discovery and Characterization of Mimivirus, the Largest Known Virus and Putative Pneumonia Agent. Emerging Infections 45: Lecture 2: Replication, Attachment and Entry 9/11 Genome Replication and Expression Sep 11, 2013: GRO-Main Campus-Bldg 200-Rotunda A Smith, A.E., and A. Helenius How Viruses Enter Animal Cells. Science 304: Bergeron, E. et al., Crimean-Congo Hemorrhagic Fever Virus Glycoprotein Processing by the Endoprotease SKI-1/S1P Is Critical for Virus Infectivity. J. Virol. 81: Lecture 3: Pathogenesis and Immunity Dr. Bungiro 9/18 Chapter 10 Sep 18, 2013: GRO-Main Campus-Bldg C (VC HD) Navarini, A.A. et al., Increased susceptibility to bacterial superinfection as a consequence of innate antiviral responses. Proc. Natl. Acad. Sci. USA 103: Sironi, M. et al., A Common Polymorphism in TLR3 Confers Natural Resistance to HIV-1 Infection. J. Immunol. 188: Simmons, C.P. et al., Dengue. New Engl. J. Med 366: Lecture 4: Antiviral Chemotherapy and Vaccines Dr. Bungiro 9/25 Chapter 10 Sep 25, 2013: GRO-Main Campus-Bldg 200-Rotunda B(VCHD) Poordad, F. et al., Exploratory Study of Oral Combination Antiviral Therapy for Hepatitis C. New Engl. J. Med 368: Zielinska, R.J. et al., Smallpox vaccine with integrated IL-15 Demonstrates enhanced in vivo viral clearance in immunodeficient mice

3 and confirs long term protection against a leathal monkeypox challenge in cynanomolgus monkeys. Vaccine. 28: H. Lai et al., Monoclonal antibody produced in plants efficiently treats West Nile virus infection in mice. Proc. Natl. Acad. Sci. 107: Lecture 5: Picornaviridae, Caliciviridae and Coronaviridae 10/2 Chapter 3 Oct 2, 2013: GRO-Main Campus- Bldg D Virgen-Slane, R. et al., An RNA virus hijacks an incognito function of a DNA repair enzyme. Proc Natl Acad Sci U S A 109: Cotton, M. et al., Full-Genomne Deep Sequencing and Phylogenetic Analysis of a Novel Human Betacoronavirus. Emerg. Infec. Dis. 19 Number 5-May 2013 (a head of print). Tan, M. and X Jiang Norovirus Gastroenteritis, Carbohydrate Receptors, and Animal Models. PLoS Path. 6(8): e doi: /journal.ppat Lecture 6 Flaviviridae, Togaviradae, Rhabdoviridae and Paramyxoviradae 10/9 Chapter 3 Oct 9, 2013: GRO-Main Campus- Bldg D Styer, L.M. et al., Mosquito Saliva Causes Enhancement of West Nile Virus Infection in Mice. J. Virol. 85: Iikow, C.S. et al., The Rubella Virus Capsid Is an Anti-Apoptotic Protein that Attenuates the Pore-Forming Ability of Bax. PLoS Pathog 7(2): e doi: /journal.ppat Nanbo, A. et al., Ebolavirus Is Internalized into Host Cells via Macropinocytosis in a Viral Glycoprotein-Dependent Manner. Plos Path. 6(9): e doi: /journal.ppat Lecture 7: Reoviridae, Bunyaviridae and Arenaviridae 10/16 Chapter 4 and 5 Midterm Exam (lectures 1-6) Oct 16, 2013: GRO-Main Campus- Bldg D Madhi, S. A Effect of Human Rotavirus Vaccine on Severe Diarrhea in African Infants. New Engl. J. Med. 362: Placios, G. et al., A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases. New Engl. J. Med. 358:

4 Yu, X-J. et al., Fever with Thrombocytopenia Associated with a Novel Bunyavirus in China. New Engl. J. Med. 364: Lecture 8: Orthomyxoviridae 10/23 Chapter 4 Oct 23, 2013: GRO-Main Campus-Bldg 200-Rotunda A Kanekiyo, M. et al., Self-assembling influenza nanoparticle vaccines elicit broadly neutralizing H1N1 antibodies. Nature online May 22. Zhu, H. et al., Infectivity, Transmission, and Pathology of Human H7N9 Influenza in Ferrets and Pigs. Science Published online 23 May 2013 [DOI: /science ] Dormitzer, D.G. et al., Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics. Sci. Transl. Med. Volume 5 Issue 185 May 15, Lecture 9: Papillomaviridae and Polyomaviridae - Walter Atwood 10/30 Chapter 7 Oct 30, 2013: GRO-Main Campus- Bldg D Yu, G. et al., Discovery of a Novel Polyomavirus in Acute Diarrheal Samples from Children. PLoS ONE 7(11):e49449.doi: /journal.pone. White, E.A. and P.M. Howley, Proteomic approaches to the study of papillomavirus-host interactions. Virol. 435: Lecture 10: Parvoviridae, Adenoviridae and Herpesviridae Dr. Thais P. Mather 11/6 Chapter 7 Nov 6, 2013: GRO-Main Campus- Bldg D Lai, C-Y. et al., Adenovirus Serotype 3 and 7 Infection with Acute Respiratory Failure in Children in Taiwan, PLoS ONE 8(1): e53614.doi: /journal.pone Matsushima, Y. et al., Novel Human Adenovirus Strain, Bangladesh. Emerg. Infec. Dis. 18: Umbach, J.L., et al., MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mrnas. Nature 454:

5 Lecture 11: Retroviridae 11/13 Chapter 6 Nov 13, 2013: GRO-Main Campus- Bldg D Weiss, R.A. and P.K. Vogt, years of Rous sarcoma virus. J. Exp. Med. 208: Matsuoika, M. and K-T. Jeang, Human T-cell leukemia virus type 1 (HTLV-1) and leukemic transformation: viral infectivity, Tax, HBZ and therapy. Oncogene 30: Hayes, B.F. et al., Immune-Correlates Analysis of an HIV-1 vaccine Efficacy Trial. New Engl. J. Med 366: Cooper, A. et al., HIV-1 causes CD4 cell death through DNAdependent protein kinase during viral integration. Nature online June 5. Lecture 12 Poxviradae and viral vectors 11/20 Chapter 7 and 11 Nov 20, 2013: GRO-Main Campus-Bldg 200-Rotunda A Nanni, P. et al., Preclinical Therapy of disseminated HER-2+ Breast Carcinomas with a Her-2 Retargeted Herpesvirus. Plos Pathogens 9(1): e Asokan, A. et al., The AAV Vector Toolkit: Poised at the clinical Crossroads. Am. Soc. Gene Ther. 20: Moss, B Poxvirus Entry: How many Proteins Does it Take? Viruses 4: /27: No Lecture (Thanksgiving) Lecture 13 Hepadnaviridae and Hepatitis viruses Dr. Andrew Campbell 12/4 Dec 4, 2013: GRO-Main Campus- Bldg D Chapter 6 Labrique, A.B. et al., Hepatitis E, a Vaccine-Preventable Cause of Maternal Deaths. Emerg. Infect. Dis. Vol. 18, No. 9, Sept. Gane, E.J., et al., Nucleotide Polymerase Inhibitor Sofosburiv plus Ribiviran for Hepatitis C. New Engl. J. Med 368: /11: REVIEW SESSION Dec 11, 2013: GRO-Main Campus- Bldg D

6 Final Examination 12/18 Dec 18, 2013: GRO-Main Campus- Bldg D Guest Lecturers: Walter Atwood, Ph.D., Professor of Medical Science, Vice Chair MCB Department Brown University Richard Bungiro, Ph.D., Lecturer in Microbiology, Brown University Andrew Campbell, Ph.D., Professor of Medical Science, Brown University Thais P. Mather, Ph.D., Associate Director of Preclinical Curriculum, Alpert Medical School of Brown University