Introduction to Virology 2037 PDF

Introduction to Virology & Virus structure and classification BMS2037 (Cellular Microbiology and Virology) Dr Marine Petit [email protected] My Profile Dr. Marine Petit Call me Marine Researcher in virology: Studying Tick-borne viral diseases Teacher in virology: Sharing my knowledge with YOU...

Introduction to Virology & Virus structure and classification BMS2037 (Cellular Microbiology and Virology) Dr Marine Petit [email protected] My Profile Dr. Marine Petit Call me Marine Researcher in virology: Studying Tick-borne viral diseases Teacher in virology: Sharing my knowledge with YOU!!! She/her Virology at Surrey • BMS1026 • Introduction to virology, an understand of the global virome and diseases caused by viruses. • BMS2037-Cellular Microbiology and Virology • How viruses infect cells, how they replicate. Important viral pathogens, how they cause disease and how they are diagnosed. • BMS3079- Human Microbial Diseases • Different routes of virus transmission. Pathogenesis and immune responses to infection. • BMS3073- Epidemiology of Infectious Diseases • Virus emergence & zoonosis. Antiviral drugs • BMS3048- Research Project Virology Lectures in BMS2037 • Introduction to Virology & Virus structure and Classification • Clinical Virology and diagnostics • Virology practical • The infectious cycle of virus replication mechanisms • Gastroenteritis viruses • Respiratory viruses • Zoonotic viruses Intro to Virology Learning Outcomes • What is a virus? • What are the characteristics of different viruses? • How are they classified? • The viral life cycle • Why and how do we research viruses? What is a virus? A virus is an obligate intracellular parasite comprising genetic material (DNA or RNA), often surrounded by a protein coat (capsid), sometimes a membrane (envelope). Important info! What is a virus? Genetic material (DNA or RNA) The virus genetic material contains the instructions for making new copies of the virus Protein coat, named capsid The capsid contains the virus genetic material Lipid membrane, named envelope The viral envelope is made from fatty lipids molecules taken form the host cells. Surface proteins Important info! These help the virus recognise and bind to cells in the host organism What is a virus? All viruses have: Some viruses have an envelope: • Viral genome: DNA or RNA • Viral Capsid: A protein coat Envelope = lipid bilayer with glycoproteins, can help virus bind to cells Important info! What is a virus? All viruses have: • Viral genome: DNA or RNA • Viral Capsid: A protein coat Important info! Enveloped viruses are less resistant to environmental constrain than non-enveloped. The Capsid Capsid main role is to protect the viral genomic material. • DNA and RNA (especially RNA!) are fragile to things such as pH, heat, drying, UV • Ensuring delivery of the genomic material into the cell Host cell recognition • Proteins on the capsid can be recognised by host cell receptors Structure of the capsid Capsid form and assembly 3 capsid forms: Helical Icosahedric Scaffolded icosahedric Capsid assembly: formation of the capsid shell. Packaging: viral genome placement inside a capsid or an envelope. Virology.org The Capsid • Closed 3-dimensional structure • No holes - Stable • Built of repeating protein structures The Capsid Capsomers Example of viral symmetry How do we study viral capsids ? Capsomers CryoEM : Transmission electron cryomicroscopy Bonus info! Viral Envelope A lipid bilayer Involved with virus attachment to cells Envelope proteins recognised by cellular receptors Can fuse with the hose cell membrane Virus can exit cells using the cell machineryCan avoid cell damage (potentially avoiding the immune response!) Enveloped vs non-enveloped Non-enveloped viruses are more resistant to pH, heat, dryness, alcohol, soap! Non-enveloped viruses *usually* cause more cellular damage. When exiting cells they disrupt the integrity of the membrane and can cause cell lysis. Enveloped Non-Enveloped Definitions to learn! Capsid: a protein coat that encloses and protects the genetic material/genome. Capsomers: clusters of proteins that compose The capsid Envelope: a lipid bilayer that surrounds the capsid of some viruses. Peplomers: Proteins on the envelope of the virus (like Glycoprotein) A Complete virus particle is called a VIRION Important info! Knowing the structure of viruses is important! Can help in creating treatments Can help in developing vaccines Knowing what kills the viruses (soap, alcohol, bleach) Virus classification Viruses are classified into a taxonomic system ICTV are responsible https://ictv.global/ Grouped by phenotypic characteristics Morphology Nucleic acid type (DNA/RNA) Replication Host Disease caused Baltimore classification system: 7 different groups based on nucleic acid, sense, method of replication Important info! Where virus names are from? Naming viruses = viruses are named after the disease they cause, for the organisms they infect, the place where it was first found, after scientist who first identified the virus. Poliovirus name come from the poliomyelitis disease Hepatitis, this term traces to the Ancient Geek noun hepar, meaning “liver”, because the disease inflames the liver’s tissue Zika virus name come from the Zika forest in Uganda where the virus was isolated in 1947 Epstein-Barr virus was named after M-A Epstein and Yvonne Barr scientist who discovered the virus Rous Sarcoma virus is a combination of all the above Classification of viruses Order …virales Picornavirales …viridae …virus …virus …virus Baltimore Classification Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. Important info! Viralzone.org Classification of viruses: summary We don’t know all properties of viruses or all known viruses We do not know if viruses have a one common ancestor Viruses can mutate and change Polythetic classification (as opposed to monothetic!) No single property but a portfolio of properties: target cells, biochemistry, structure and mainly now genome sequences Related viruses share many of these, but often not all. 5 minute break Viruses are everywhere! Viruses infect all living things-even bacteria! Viruses outnumber bacteria 10:1 Bacteriophage Estimate of 320,000 types of viruses-for now! We would likely not exist without viruses The Human Virome ~ 5.10+6 hairs ~ 1.10+13 cells ~ 1.10+14 bacteria ~ 1.10+15 viruses 5-8% of our DNA is made of virus genetic material (endogenous virus) acquired during evolution through infection of germ cells. The infectious life cycle Some important definitions • A susceptible cell has a functional receptor for a given virus - the cell may or may not be able to support viral replication • A resistant cell has no receptor - it may or may not be competent to support viral replication • A permissive cell has the capacity to replicate virus - it may or may not be susceptible • A susceptible AND permissive cell is the only cell that can take up a virus particle and replicate it Important info! Virus particles are metastable Stable enough to protect the genome Capsid structure is symmetrical- proteins fit tightly together and provide stability Unstable enough to come apart following infection Bonds are not permanent (usually non-covalent) Following infection, the capsid comes apart to expose genomic material Infectious Cycle We break it down into stages, so it is easier to understand! Very simply the viral life cycle is: 1. Attachment to cells 2. Enter & uncoating 3. mRNA 3. Translation using host ribosomes 4. Assembly 5. Egress (exit) Important info! Viral diseases Pathogenesis Pathogenesis From the Greek for Suffering/disease creation Viral Pathogenesis: the process by which a virus causes a disease Effects of the viral infection and replication + Effects of host response (immune system) Important info! = DISEASE Viral Virulence Capacity of a virus to cause disease in a host Virulence can be quantitated: - Virus titer - Mean time to death - Mean time to appearance of signs - Measurement of fever, weight loss Many signs/symptoms of disease are caused by immune response! Symptoms = What only you can feel Signs = what others detect Important info! Viral Virulence Virulence can be quantitated: - Virus titer (B) - Mean time to death (A) - Mean time to appearance of signs - Measurement of fever, weight loss Principle of virology, ASM press Viral Virulence is a relative property Influenced by dose, route of infection, species, age, sex, and susceptibility of host Not correct to compare virulence of different viruses For similar viruses assays must be the same Virulence depends on the route of inoculation: Principle of virology, ASM press The Burden of Viral Disease-human 2-3 million Deaths each year Enterovirus Measles Diarrheal and vomiting (in conjunction with malnutrition) 10 % of child Mortality in developing world Influenza 1918 pandemic AIDS (HIV) 2012: 34 million infected, 2.9 million became infected and 2.1 million died. 20 million deaths Current pandemic * *Average life expectancy now <40yrs in sub-Saharan Africa due to AIDS Viruses also affect plants, animals, insects... Plant viruses cause ~£40 billion worth of crop losses a year Livestock diseases result in huge losses to the farming industry Tomato Spotted Wilt Virus Impact on wild animals or domesticated animals ? Foot and mouth Felines-SARS, SARS-CoV-2 What pets were affected in the recent monkeypox outbreak? Important info! Bluetongue virus ~$3 billion/year How do viruses affect us? Acute infection Long-term infections Oncogenesis Economic impact Can you think of an example of each of these? How do viruses affect us? Less trade & transportation Reduce tourism High unemployment Decrease agricultural production High fiscal impact Economic impact of Ebola Outbreak Fewer investors Decrease mining Mercycorps.org Can viruses be beneficial? Oncolytic viruses Alternatives to antibiotics Gene therapy Biological control-an alternative to pesticides? Why bother looking for new viruses? Causes of human disease Potential zoonotic viruses-pandemic potential? Identifying good viruses? Phages? Through the discovery of 214 new RNA virus, Holmes team has determined that viruses infecting us today have ancient evolutionary histories that date back to the first vertebrates and perhaps the first animals in existence. Holmes et al. 2018 Why bother looking for new viruses? Emerging virus and new virus research is key to Pandemic preparedness A virus is an obligate intracellular parasite comprising genetic material (DNA or RNA), often surrounded by a protein coat (capsid), sometimes a membrane (envelope). Must having living appropriate cells to study viruses! Important definition to learn! Obligate Parasites Obligate Parasites Viruses hijack the cell “factory” (cellular pathways) for their own benefits (replication + dissemination) No cell = No virus Important info! Scale of viruses Open Oregon Press Books Growing Viruses HeLa cells HEp-2 cells Growing Viruses In 1913 vaccinia was grown in cell culture Enders, Weller & Robbins awarded Nobel prize in 1954 for ability to grow poliovirus in human cells. First virus isolated in 1950 (poliovirus) Today: Innovative cell culture technique like 3D culture Cell culture- cytopathic effect Sars-Coronavirus 2 infection in cell culture Important CytoPathic Effect-- CPE Little to No CytoPathic Effect-- CPE Tastan et al. 2020 Cell culture- cytopathic effect Sars-Coronavirus 2 infection in cell culture Important CytoPathic Effect-- CPE Little to No CytoPathic Effect-- CPE Tastan et al. 2020 Non-infected cells Usutu infected cells Bayonki et al. 2005 CPE and viral titration– Plaque assay Principle of Virology, ASM Press 1952, Renato Dulbecco developed plaque assay for animal viruses Nobel Prize, 1975 CPE and viral titration– Plaque assay Principle of Virology, ASM Press 1952, Renato Dulbecco developed plaque assay for animal viruses Nobel Prize, 1975 New tools for virology Research: Organoids Human intestinal organoids infected with SARS-CoV-2 (white). Pic: Joep Beumer/Clevers group/Hubrecht Institute Key Points: • Understand how viruses are classified • Learn key definitions of a virus and parts of the virion • Understand the steps in the viral life cycle • Appreciate the burden of viral disease • Know that viruses are obligate intracellular parasites and can only grow in susceptible & permissive cells Virology – useful sources • • • • • • • • • Principles of Virology Fields Virology What is a virus? https://www.youtube.com/watch?v=8FqlTslU22s For a more in-depth exploration of virus structures https://www.youtube.com/watch?v=KoJWuWzVgqQ TWIV (podcast!) Viralzone http://viralzone.expasy.org/ All the Virology on the WWW http://www.virology.net/ The big picture book of viruses http://www.virology.net/Big_Virology/BVHomePage.html International committee on taxonomy of viruses http://www.ictvonline.org/