Introduction To Viruses PDF

Introduction to Viruses Instructor: Craig McCormick, Ph.D. Professor Department of Microbiology & Immunology email: [email protected] Overview of the MICI2100 Virology block Oct. 2 Introduction Oct. 4 Virus Structure Oct. 9 Virus Entry Oct. 11 Virus Genome Replicati...

Introduction to Viruses Instructor: Craig McCormick, Ph.D. Professor Department of Microbiology & Immunology email: [email protected] Overview of the MICI2100 Virology block Oct. 2 Introduction Oct. 4 Virus Structure Oct. 9 Virus Entry Oct. 11 Virus Genome Replication (part 1) Oct. 16 Virus Genome Replication (part 2) Oct. 18 Viral Assembly and Egress Oct. 23 Viral Genetics and Evolution Oct. 25 MIDTERM #2  Viruses are amazing They are simple machines that have evolved to replicate in certain hosts. – sometimes this results in disease - many examples of benign or beneficial viruses in nature Study of viruses has potential to: - aid disease prevention - help us understand fundamentals of host biology  Goals Fundamentals of virology: - What is a virus? - What does it look like? - How does it replicate in host cells? - What are some host cell defenses against viruses? - How do new viruses emerge? Methods: How do we examine viruses? Drill down on specific viruses: - poliovirus - Influenza virus - HIV - SARS-CoV-2  Learning Resources - Viruses - Lots of misinformation about viruses in mainstream media - good resources include : - The NCBI, a searchable archive of peer-reviewed medical research http://www.ncbi.nlm.nih.gov/ -TWIV: this week in virology - Part of a collection of microbiology podcasts on Microbe.tv  Learning Resources – Global Surveillance - ProMEDmail.org - MMWR – the Morbidity and Mortality Weekly Report Where are viruses?  Viruses are everywhere We eat and breathe billions of them regularly We breathe 6L of air per minute Eat several kg of food per day Touch everything (doorknobs, elevator buttons, etc.) We put our fingers in our eyes and mouths Every milliliter of seawater has at least 10 million virus particles We carry viral genomes as part of our own genetic material Viruses infect our pets, domestic food animals, wildlife, plants, insects Viral infections can cross species barriers, and do so constantly (zoonotic infections)  Marine viruses affect the global carbon cycle Microbes represent large majority of biomass in the ocean Viruses are the most abundant entities in global ecosystems Approx. 1030 viruses in the oceans Same amount of carbon as 75 million blue whales  The Suttle lab at UBC Researching ocean viruses Impact on the carbon cycle  Viruses infect marine mammals Whales are commonly infected with a tiny virus of the calicivirus family Causes rashes, blisters, diarrhea Infected whales can shed 1013 viruses per day! Also…whale herpesviruses, poxviruses, orthomyxoviruses, paramyxoviruses  How ‘infected’ are we? Amazingly, the majority of the viruses that infect us are completely innocuous Each person in this room is probably infected with at least 2 of the 8 known human herpesviruses HSV-1, HSV-2,VZV, HCMV, EBV, HHV-6, HHV-7, HHV-8 Persistent, life-long infection The human virome  Ancient Viral Infections Viruses have been with us since the beginning: - no fossil record for viruses, but their presence is evident in genomes of vertebrates - Retroviruses integrate into host genomes - 10% of the human genome consists of retrovirus-like sequences!! - Similar findings in other genomes (mouse, rat, etc.) - Suggests that these viruses have been infecting vertebrates for approx. 100 million years! - How are these viral sequences ‘fixed’ in the human genome?  Retrovirus in process of being ‘fixed’ in host genome Koala retrovirus (KoRV) Infectious cause of Koala Immune Deficiency Syndrome (KIDS) KoRV is being ‘endogenized’ in Koala genome Virus can spread ‘horizontally’ and ‘vertically’ Do these integrated ancient viruses do anything?  construct was co-transfected to normalize for transfection efficiency. Received 13 October; accepted 21 December 1999.................................................................. 1. Cadigan, K. M. & Nusse, R. Wnt signaling: a common theme in animal development. Genes Dev. 11, Syncytinisa captive retroviral Viral genes influenced human 3286–3305 (1997). 2. Heldin, C. H., Miyazono, K. & ten Dijke, P. TGF-! signalling from cell membrane to nucleus through SMAD proteins. Nature 390, 465–471 (1997). envelope proteininvolved evolution 3. Massagué, J. TGF-! signal transduction. Annu. Rev. Biochem. 67, 753–791 (1998). 4. Harland, R. & Gerhart, J. Formation and function of Spemann’s organizer. Annu. Rev. Cell Dev. Biol. 13, 611–667 (1997). inhumanplacental morphogenesis 5. Brannon, M., Gomperts, M., Sumoy, L., Moon, R. T. & Kimelman, D. A !-catenin/XTcf-3 complex Sha Mi, Xinhua Lee, Xiang-ping Li, Geertruida M. Veldman, binds to the siamois promoter to regulate dorsal axis specification in Xenopus. Genes Dev. 11, 2359– Heather Finnerty, Lisa Racie, Edward LaVallie, Xiang-Yang Tang, Syncytin is a viral gene belonging to 2370 (1997). 6. Moon, R. T. & Kimelman, D. From cortical rotation to organizer gene expression: toward a molecular Philippe Edouard, Steve Howes, James C. Keith Jr & John M. McCoy* explanation of axis specification in Xenopus. BioEssays 20, 536–545 (1998). ‘endogenous retrovirus’ 7. Watabe, T. et al. Molecular mechanisms of Spemann’s organizer formation: conserved growth factor synergy between Xenopus and mouse. Genes Dev. 9, 3038–3050 (1995). Genetics Institute, Inc., 87 CambridgePark Drive, Cambridge, Massachusetts 02140, USA 8. Laurent, M. N., Blitz, I. L., Hashimoto, C., Rothbacher, U. & Cho, K. W. The Xenopus homeobox gene twin mediates Wnt induction of goosecoid in establishment of Spemann’s organizer. Development 124, *Present address: Biogen Inc., 14 Cambridge Center, Cambridge, 4905–4916 (1997). Massachusetts 02142, USA Ancient cell attachment protein 9. Crease, D. J., Dyson, S. & Gurdon, J. B. Cooperation between the activin and Wnt pathways in the spatial control of organizer gene expression. Proc. Natl Acad. Sci. USA 95, 4398–4403 (1998)............................................................................................................................................... Many mammalian viruses have acquired genes from their hosts 10. Candia, A. F. et al. Cellular interpretation of multiple TGF-! signals: intracellular antagonism between activin/BVg1 and BMP-2/4 signaling mediated by Smads. Development 124, 4467–4480 (1997). during their evolution1. The rationale for these acquisitions is 11. Lagna, G., Hata, A., Hemmati-Brivanlou, A. & Massagué, J. Partnership between DPC4 and SMAD usually quite clear: the captured genes are subverted to provide a Located in human chromosome 7 proteins in TGF-! signalling pathways. Nature 383, 832–836 (1996). 12. Hoodless, P. A. et al. Dominant-negative Smad2 mutants inhibit activin/Vg1 signaling and disrupt selective advantage to the virus. Here we describe the opposite situation, where a viral gene has been sequestered to serve an axis formation in Xenopus. Dev. Biol. 207, 364–379 (1999). 13. Shi, Y. et al. Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in important function in the physiology of a mammalian host. This TGF-! signaling. Cell 94, 585–594 (1998). gene, encoding a protein that we have called syncytin, is the Essential for placental development 14. Yost, C. et al. The axis-inducing activity, stability, and subcellular distribution of !-catenin is regulated in Xenopus embryos by glycogen synthase kinase 3. Genes Dev. 10, 1443–1454 (1996). envelope gene of a recently identified human endogenous defec- tive retrovirus, HERV-W2. We find that the major sites of syncytin 15. Waterman, M. L. & Jones, K. A. Purification of TCF-1", a T-cell-specific transcription factor that activates the T-cell receptor C" gene enhancer in a context-dependent manner. New Biol. 2, 621–636 expression are placental syncytiotrophoblasts, multinucleated (1990). 16. Fujita, T., Nolan, G. P., Liou, H. C., Scott, M. L. & Baltimore, D. The candidate proto-oncogene bcl-3 encodes a transcriptional coactivator that activates through NF-kappa B p50 homodimers. Genes Dev. 7, 1354–1363 (1993). 17. McKendry, R., Hsu, S. C., Harland, R. M. & Grosschedl, R. LEF-1/TCF proteins mediate wnt- inducible transcription from the Xenopus nodal-related 3 promoter. Dev. Biol. 192, 420–431 (1997). 18. He, T. C. et al. Identification of c-MYC as a target of the APC pathway. Science 281, 1509–1512 (1998). 19. Tetsu, O. & McCormick, F. !-catenin regulates expression of cyclin D1 in colon carcinoma cells. Nature 398, 422–426 (1999). 20. Christian, J. L. & Moon, R. T. Interactions between Xwnt-8 and Spemann organizer signaling pathways generate dorsoventral pattern in the embryonic mesoderm of Xenopus. Genes Dev. 7, 13–28 (1993). 21. Jones, C. M., Lyons, K. M., Lapan, P. M., Wright, C. V. & Hogan, B. L. DVR-4 (bone morphogenetic protein-4) as a posterior-ventralizing factor in Xenopus mesoderm induction. Development 115, 639– 647 (1992). 22. Hoppler, S. & Moon, R. T. BMP-2/-4 and Wnt-8 cooperatively pattern the Xenopus mesoderm. Mech. Dev. 71, 119–129 (1998). 23. Riese, J. et al. LEF-1, a nuclear factor coordinating signaling inputs from wingless and decapentaplegic. Cell 88, 777–787 (1997). 24. Theisen, H., Haerry, T. E., O’Connor, M. B. &Marsh, J. L. Developmental territories created by mutual antagonism between Wingless and Decapentaplegic. Development 122, 3939–3948 (1996). 25. Brook, W. J. & Cohen, S. M. Antagonistic interactions between wingless and decapentaplegic  Captured viral gene essential for placental development Syncytin creates fused syncytiotrophoblast layer Required to maintain semipermeable barrier between mother and fetus during pregnancy  It works both ways: viruses capture human genes KSHV is a human herpesvirus Genes in yellow are captured from our primate ancestors  Summary Viruses can co-evolve with their hosts There is exchange of genetic information between virus and host  What IS a virus? Virus: from the Latin noun virus, meaning toxin or poison  What IS a virus? Simple definition: - Viruses are submicroscopic, obligate intracellular parasites Further: - virus particles are produced from the assembly of preformed components (other agents grow from an increase in the integrated sum of their components and reproduce by division) - virus particles (virions) themselves do not grow or undergo division - viruses lack the genetic information that encodes apparatus necessary for: a) generation of metabolic energy b) protein synthesis  Viruses employ different strategies to parasitize host cells As viruses are obligate molecular parasites, every solution must reveal something about the host as well as the virus Viruses are simple ‘Darwinian machines’ – survival of the fittest  Is it alive? Viruses challenge our definition of ‘LIFE’ - certainly viruses multiply, but they do not ‘grow’ - instead viruses harness cellular processes to direct genome replication and assembly of progeny virions One view: - inside the host cell: viruses are alive - outside of the host cell: complex assemblages of metabolically inert chemicals  Viruses come in all shapes and sizes EBOLA VIRUS Source: US Centres for Disease Control INFLUENZA VIRIONS Source: CDC, Dr. Terence Tumpey COLIPHAGE T1 Source: GrahamColm, Public Domain Most viruses are smaller than bacteria * PIN 1x * 2x 4x 6x 8x *10x *  HAIR 20x 40x  DUST MITE 60x 80x *100x * 200x 400x 600x  RAGWEED POLLEN 800x * 1000x *  LYMPHOCYTE 2000x  RED BLOOD CELL 4000x  BAKER’S YEAST 6000x  E. COLI 8000x *10,000 X *  STAPHYLOCCOUS 20,000 X 40,000 X 60,000 X  EBOLA 80,000 X *100,000 X* 200,000 X 400,000 X  RHINOVIRUS 600,000 X 800,000 X *1,000,000 X*  How to visualize viruses? Indirect method = Plaque assays - serial dilute inoculum - add to layer of susceptible cells - overlay with agar - wait for cytopathic effect (cell destruction) - plaques are holes in the single layer of cells.  How to visualize viruses? Indirect method = Plaque assays - serial dilute inoculum - add to layer of susceptible cells - overlay with agar - wait for cytopathic effect (cell destruction) - plaques are holes in the single layer of cells.  Electron Microscopy Direct method: Electron Microscopy is a powerful method to visualize viruses Electrons pass through a stained, ultrathin sample Tour of Electron Microscopy Unit Mary Ann Trevors, Technician  Summary - Viruses are submicroscopic, obligate intracellular parasites -Viruses have a big impact on the web of life (infecting animals, bacteria, amoeba, etc.) -Viruses exchange genetic information with their host organisms -We are covered with a virome -Not all viruses are pathogenic; humans are thriving in a world full of viruses -Most viruses can not be visualized by conventional microscopy - EM is a powerful technique for visualizing viruses - Plaque assays are indirect method to detect viruses  Your Homework - Go on TWIV and listen to a podcast. - Next class: share what you learned and get a prize!