Introduction to Virology Lecture 1 PDF

Introduction to Virology, Lecture 1 Dr Craig Thompson Assistant Professor of Molecular Pathology Learning outcomes Describe the key elements that define a virus. Describe the key experiments iden@fying viruses. Describe the characteris@cs of the structure of viruses (esp. influenza,...

Introduction to Virology, Lecture 1 Dr Craig Thompson Assistant Professor of Molecular Pathology Learning outcomes Describe the key elements that define a virus. Describe the key experiments iden@fying viruses. Describe the characteris@cs of the structure of viruses (esp. influenza, varicella, SARS-CoV-2). Describe the characteris@cs of the infec@ous cycle (esp. influenza, varicella, SARS-CoV-2). Define terms describing viral infec@on: latency, chronic ac@ve, persistence. Describe pathogenesis of viral infec@on (esp. influenza and varicella).  Viruses We live in a cloud of viruses. Viruses infect every living thing. We regularly eat and breathe in billions of virus par8cles. We carry viral genomes as part of our own gene8c material. A bacteriophage A thought experiment: There are more than 1030 bacteriophage par@cles in the world’s waters (NB: a bacteriophage is a virus that infects bacteria) A bacteriophage weighs a femtogram (10-15) then: Earth 10-15 x 1030 = 1015 grams = 1012 kg The weight of all the people in the UK is 5.29 x 109 kg (67.5 million people) The weight of the popula@on of Europe is 3.512 x 1010 kg (445 million people) The weight of the popula@on of the world is 6.3 x 1011 kg (8 billion people)  Viruses in a litre of sea water There are more viruses in a litre of sea water than there are people on earth. Abundance = par@cle number. Nat Rev Microbiol 5, 801–812 (2007)  Viruses – Infect us. Human Virome Once infected some viruses are for life. For example: Herpes simplex virus 1 & 2 (HSV1, HSV-2) Varicella zoster virus (VZV) - otherwise known as chickenpox Human cytomegalovirus (HCMV) Epstein–Barr virus (EBV) And Human herpesvirus 6, 7 & 8 (HHV-6, HHV-7, HHV-8) Nat Rev Microbiol 19, 514–527 (2021)  Viruses –Disease Viruses cause a great amount of human disease. Our World in Data  Viruses –Disease Viruses cause a great amount of human disease. Deaths Flu SARS-CoV-2 HIV Flaviviruses Norovirus per year 250,000-600,000 3,000,000 680,000 100,000 200,000 (approx) Source: WHO WHO UNAIDS Lancet CDC  Infec8ous Diseases Impact Low and Middle Income Countries to a far greater extent than Higher Income Countries World Health Organisa@on  Viruses – Could they also be beneficial?. Gene regula*on: Very lidle of our genome is made up of protein coding genes. A lot of the human genome is made from integrated retroviruses in the form of transposons – LINEs, SINEs. Viruses can insert into the genome and regulate associated genes. However, there’s s@ll much we don’t know about this phenomenon. Placenta: The placenta is made from viral protein – the syncy@n gene makes the placenta (see diagram on the next slide). Long interspersed nuclear element = LINEs Vaccines: Short interspersed nuclear element = SINEs Viruses can also be used as vaccine vectors, eg the ChadOx COVID-19 vaccine based on an adenoviral vector. Nat Rev Genet 10, 691–703 (2009).  The role of viral gene regula8on and protein co-op8on in placenta forma8on PLoS Biol 2018 16(10):e3000028.  In these two introductory lectures we will focus on principles - Ideas and approaches that can be applied to every virus  Defini8on Virus. “An infec@ve agent that typically consists of a nucleic acid molecule in a protein coat, is too small to be seen by light microscopy, and is able to mul@ply only within the living cells of a host.” The Oxford English Dic@onary  The Nature of Viruses Not considered cells No metabolism of their own Rely completely on biosynthe@c machinery of infected cell “Organisms at the edge of life” or merely “infec@ous chemicals”? Infect all types of cells Plant, animal, pro@sts, archaea, bacteria 10nm-700nm in diameter Filoviruses length ≤1400 nm Principles of Virology A Brief History of Virology “Virus” originally meant poison 1920s Thomas Milton Rivers book Filtrable Viruses 1880s Pasteur speculated that rabies pathogen too small to be detected by light microscope “Viruses appear to be obligate parasites in the sense that their reproduction is dependent on 1892 first “filterable virus” living cells." tobacco mosaic virus detected by Ivanovsky, but 1931 electron microscope invented thought to be toxin Beijerinck suggests name virus for filterable 1933 Influenza infectious agent 1948-55 Cell Culture 1898 first animal virus: Foot & mouth disease 1952 Poliovirus virus 1969 Hepatitis B 1901 Yellow fever discovered (virus isolated in 1932) 1983 HIV 1903 Rabies 1989 HCV Early 20th Century Twort and D’Herelle’s work on bacteriophages Key Experiments Iden7fying Viruses  Key Experiment 1: Viruses aren’t bacteria These experiment revolved around the “Chamberlain Filter”. This showed that viruses were (i) microscopic, (ii) required a host to replicate. In 1884, Charles Chamberlain developed a filter to remove bacteria from drinking water. Tobacco was a major crop in the 1900s and was periodically affected by pathogen outbreaks (in this case tobacco mosaic virus). Consequently ground tobacco was filtered using the Chamberlain filter to determine if bacteria were responsible for the outbreaks. It was found that the filtrate was s@ll able to infect tobacco plans, indica@ng that the detrimental agent were smaller than a bacteria. Pasteur also found that the agent causing rabies passed through the filter However, it was s8ll unclear if viruses were toxins or microorganisms.  Key Experiment 2: Viruses are microscopic The first EM The development of the electron microscope enabled scien@sts to determine that viruses microscope were microorganisms made up of organised proteins and nucleic acids. Helmut Ruska in 1939 was the first person to visualise viruses (his brother made the first EM microscope). One of the first EM pictures of virus However, we s8ll did not know whether viruses had a nucleic acid genome. Lancet 2000 355(9216):1713-7  Key Experiment 3: Nucleic acid is the heritable material Known as the Hershey–Chase experiment: Hershey and Chase inserted the radioac@ve elements in the bacteriophages by adding the isotopes to separate media within which bacteria were allowed to grow. When the bacteriophages infected the bacteria, the progeny contained the radioac@ve isotopes in their structures. This procedure was performed once for the sulfur-labeled phages and once for phosphorus-labeled phages. The labeled progeny were then allowed to infect unlabeled bacteria. The phage coats remained on the outside of the bacteria, while gene@c material entered. Disrup@on of phage from the bacteria by agita@on in a blender followed by centrifuga@on allowed for the separa@on of the phage coats from the bacteria. These bacteria were lysed to release phage progeny. The progeny of the phages that were labeled with radioac@ve phosphorus remained labeled, whereas the progeny of the phages labeled with radioac@ve sulfur were unlabeled. Thus, the Hershey–Chase experiment helped to confirm that DNA, not protein, is the gene@c material. Key Experiment 3: Nucleic acid is the heritable material  Question 1: How did we discover that viruses were micro-organisms? The Structure of Viruses  Structure of Viruses Genetic core DNA or RNA never both Protein coat or capsid Individual units Capsomeres Envelope only some viruses  Classifica8on Ebola Herpesvirus SARS Adenovirus HIV Papillomavirus Influenza Principles of Virology Differences between bacteria and viruses Viruses: Bacteria: Obligate intracellular parasites Usually free-living, but can be No ribosomes, metabolism parasites DNA or RNA, not both Ribosomes, metabolism seen by EM [20-400nm] DNA and RNA 10-100s of genes seen by LM [1000nm] Tangled phylogeny 100s-1000s of genes Natural phylogeny  Bal8more classifica8on Developed by David Baltimore Groups viruses into families depending on: Type of genome: DNA, RNA, single-stranded (ss), double- stranded (ds) etc. Method of viral mRNA synthesis and replication Principles of Virology  Bal8more Classifica8on I. dsDNA viruses e.g. Adenoviruses, Herpesviruses, Poxviruses II. ssDNA viruses (+)sense DNA e.g. Parvoviruses III. dsRNA viruses e.g. Retroviruses 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; retroviruses exploit a reverse transcriptase to copy information from RNA genome into DNA VII. dsDNA-RT viruses e.g. Hepadnaviruses  Diversity of Viruses Principles of Virology Hepa@@s B: special case because has reverse transcriptase  Question 2: What type of virus is influenza as per the Bal@more classifica@on? The Infec7ous Cycle Defini8on Everything that happens to and within a virus infected cell.  The Infec8ous Cycle cuvvvrr Translocation - e.g. polio Endocytosis - e.g. influenza Receptor Fusion - e.g. Parainfluenza and HIV binding Release Cell entry Virion assembly Uncoa@ng Viral genome RNA viruses use virus-specified Viral protein replica@on synthesis enzymes & transcrip@on DNA viruses use host cell enzymes  Stages of infec@on: 1. A9achment and Entry: 2. Transla>on 3. Genome replica>on 4. Release We will go into much more details into these areas in the next lecture! Principles of Virology hdps://www.youtube.com/watch?v=k2GlafQ9YhY  Questions 3 & 4: What type of glycoprotein does SARS-CoV-2 use to enter cells? & What is it’s receptor?  Viruses: effects on cells Death Cytopathic effect (CPE) Transformation Leads to malignant cells Latent infection Virus remains within cells without harm Principles of Virology Key terms: A suscep>ble cell has func@onal receptor of a given virus – the cell may or may not be able to support viral replica8on. A resistant cell has no receptor – it may or may not be competent to support viral replica@on. A permissive cell has the capacity to replicate virus – it may or may not be suscep@ble. A suscep>ble AND permissive cell is the only cell that can take up virus and allow it to replicate. Principles of Virology  Viruses: Natural history of infec8on Different types of infec@on Acute Primary infec@on usually followed by las@ng immunity Chronic/Persistent Primary infec@on followed by a slow smouldering infec@on Latent Primary infec@on followed by restricted viral gene expression  Viruses: Persistence Host cell infec>on without cell death infec@on of non-permissive cells evolu@on of viral variants Long-term maintenance of viral genome integra@on of viral genome into host genome (e.g. HIV) OR episomal circular molecules Avoidance of host immune system Restricted expression of viral genome An@genic varia@on leads to escape mutants  Natural history of viral infec8ons: Acute Infectious period Incuba@on Symptoms Post-symptoma@c infec@on Acute primary infec@on (influenza or chickenpox) Acute secondary infec@on (shingles) Virus levels Time: days to weeks  Natural history of viral infec8ons: Acute followed by Chronic Incuba@on Symptoms Symptoms Virus levels Time: days-weeks months-years Acute primary followed by chronic latent (Herpesviruses)  Question 5: What is the difference between acute and chronic infec@on? Pathogenesis Defini8on The manner of development of a disease.  Influenza pathogenesis Host cell entry specific binding to receptors in the respiratory tract Cytopathy lysis of ciliated and mucus-secre@ng respiratory epithelial cells Host protec>ve responses an@body important in future protec@ve immunity (vaccina@on) Immunopathology interferon and other cytokines cause chills and aches  Varicella pathogenesis Host cell binding and entry inhala@on, infects tonsils and mucosa of URT Stability in the body/ compartment infects T cells which deliver virus to skin Con>guous infec>on of adjacent cells bloodstream and lympha@c spread Cytopathy syncy@a form in epithelia Host protec>ve responses virus cleared by cell-mediated immunity latently infected cells are not recognised by immune system Immunopathology Latent infec@on in neurons usually dorsal root and cranial ganglia  Mul8ple Routes of Entry Routes of infection: Ingestion Inhalation Sexual Inoculation Transfusions and transplants Congenital /Vertical Principles of Virology