MIMM 211 Introductory Microbiology Lecture 1 2024 PDF

Lecture 1 Introduction to Virology MIMM 211 – Introductory Microbiology Friday November 1st, 2024 Dr. Jasmin Chahal 6  Register for Slido We will be doing some...

Lecture 1 Introduction to Virology MIMM 211 – Introductory Microbiology Friday November 1st, 2024 Dr. Jasmin Chahal 6  Register for Slido We will be doing some interactive polling questions! Live polls using Slido: https://www.mcgill.ca/polling/ or sign in via Webex Enter # 3031727 1 https://calendly.com/jros ealford/misa-headshot- fundraiser 2 https://www.zeffy.com/en- CA/ticketing/3a74be7a- 4ce5-459d-8e5e- 1abf6b41aed3 3 https://www.zeffy.com/en- CA/ticketing/4d592568-7e52- 4b4d-9a08-a7b23131b8ec 4  Land Acknowledgment McGill University is on land which has long served as a site of meeting and exchange amongst Indigenous peoples, including the Haudenosaunee and Anishinabeg nations. We acknowledge and thank the diverse Indigenous peoples whose presence marks this territory on which peoples of the world now gather. For video, please visit: https://www.youtube.com/watch?v=uq_fbdEVRmM 5  Administrative Information (I) How to reach me: - Email: [email protected] - Office: Room 408A, Duff Medical Building - Office hours: By appointment on Calendly https://calendly.com/jasmin-chahal/winter-2024-clone Email policy: - If your question is about content or assessments, please explain what steps you previously took to get an answer to your question (i.e. discussion board) - I will do my best to answer quickly but it can take a few days 7  Administrative Information (II) Previously taught by Dr. Jacques Archambault - Currently teaching MIMM 324 - Research on Human Papillomaviruses - Some slides are adapted from his lectures 8  Lecture content for this module Lecture slides will be posted the day before All the content for the final is in the lecture slides - I might give some hints throughout the lectures…. Content: - Overview of viruses - Virus Structure, Genomes and Classification - Genome Classification - The Infectious Cycle - Cultivation and Detection of Viruses - Viruses and Cancer + Some pathogenetic viruses 9  Resources Wellness Hub: https://www.mcgill.ca/wellness-hub/ - Fanny Gutierrez-Meyers (Local Wellness Advisor): [email protected] Office for Sexual Violence Response, Support and Education: https://mcgill.ca/osvrse Laptop loaning: https://mcgill.service- now.com/itportal?id=kb_article&sysparm_article=KB0010885  go to “Audiovisual Equipment loans” (2 business days in advance) 10 A bit about me 11  Please download and install the Slido app on all computers you use Check-in: How are you? ⓘ Start presenting to display the poll results on this slide. 12  Please download and install the Slido app on all computers you use Virus trivia: Check all the statements that you think are true ⓘ Start presenting to display the poll results on this slide. 13  Why is it important to study viruses? They make up most of Earth’s living matter - Scientists estimate that 10 quintillion virus particles populate the planet (that’s one followed by 31 zeros!) - Influence diversity and evolution We carry viral genomes as part of our own genetic material Can be harmful to hosts  diseases, epidemics or cancer Can enhance health of hosts Provide tools and model systems for our discovery of the fundamental principles of molecular biology We can now engineer viruses to deliver gene therapy and kill cancers or deliver vaccines Most identified DNA sequences floating in our blood plasma belong to viruses! 14 Science news 11 Jan 2014; Popgeorgiev, Nikolay et al., The Journal of Infectious Diseases (2013) What do we know about viruses? 15  General characteristics of viruses (I) Virus: genetic element that can multiply only in a living (host) cell - Not living, cannot reproduce independently - Obligate intracellular parasite: Needs host cell for energy, metabolic intermediates, protein synthesis Virus particle (virion): extracellular form of a virus - Exists outside host and facilitates transmission from one host cell to another Replication/reproduction occurs only upon infection (entry into host cell) - Cause infections in all living things (humans, animals, plants and bacteria) Contains nucleic acids – either DNA or RNA - No cytoplasmic membrane or organelles 16 Copyright Pearson (2020)  General characteristics of viruses (II) Extracellular state (virion) - Protein coat (capsid) surrounding nucleic acid - Nucleic acid and capsid = nucleocapsid - Some have phospholipid envelope Consisting of a phospholipid bilayer from host cell membrane and viral proteins May posses glycoproteins (spikes)—projections from outer surface. Recognize and bind receptor of host cell Outermost layer provides protection and recognition sites for host cells Intracellular state - Capsid removed More detail about these in - Virus exists as nucleic acid (as seen in later lectures) later lectures 17 Copyright Pearson (2020) Discovery of viruses 18  A bit of history DO NOT NEED TO KNOW DATES Late 1800s, coined the term viruses (“poison” or “slimy liquid” in Latin) In 1886, Chemist Adolf Mayer showed that tobacco mosaic disease (TMD) was transmissible from a diseased plant to a healthy plant Virus discovery: the beginning In 1892, Bacteriologist Dimitri Iwanowski filtered the sap of diseased plant through porcelain filter that was designed to retain bacteriaIdentification of viral pathogens by filtration - Found out that the infectious agent passed Viruses through are small the filter and can pass through 0.2 micron filters, unlike bacteria In 1946, Chemist Wendell Stanley earned a Nobel Other Prize for isolation, characterization and key concept crystallization of Tobacco Mosaic Virus (TMV) Viruses are not only small, but they replicate only in the host, not in bro In 1957, Bacteriologist Sarah Stewart pioneered the concept that some viruses can lead to cancer Bacteria + virus Filter of porosity that A) Healthy retains bacteria but Tobacco leaf and not viruses B) tobacco leaf infected with TMV Virus Pasteur’s 19 swan-neck Copyright Pearson (2020) Sarah Stewart in 1950  Viral Evolution/Origin To date, no definitive explanation for the origin(s) of viruses exists Viruses may have arisen either prior to or from cells,~4 billion years ago A few hypotheses: - Viruses require host cell  viruses evolved after cells first appeared - Viruses were around during the “RNA world” a period (precellular era), free living, in evolution when RNA is hypothesized to have been the sole carrier of genetic information LUCA: Last universal common ancestor 1400 BC – shortened, withered leg, one of the earliest depictions of polio Nasir et al., Trends in Microbiology (2020) 20  Why viruses appeared? Mechanism to quickly move genes Viruses enriched genetic diversity of hosts by facilitating gene transfers - Especially relevant for prokaryotic cells (horizontal gene transfer) - Possible that earliest viruses co-existed with host cells evolved killing host later - Viruses as part of the “RNA world” played a role in RNA to DNA transition? Hypothesis RNA to DNA transition: Some RNA viruses evolved DNA genomes to protect their genomes from cellular ribonucleases (cellular enzymes that destroy foreign RNA) DNA is more stable than RNA Use of cellular replication machinery to replicate 21 Copyright Pearson (2020)  Viruses are everywhere! Vast majority of viruses remain undiscovered and unidentified 22  Viruses are everywhere! Viruses occupy Viruses areallthe nearly most abundant organisms and are form foundofinbiological material virtually every type of habitat (i.e. in air and ocean) - Viruses can infect More than bacteria, fungi,inanimals, 1030 bacteriophages the world’s plants waters. Aand humans head-to-tail line of 1030 phages is 100 million light years! Viruses are the most abundant microorganism on this planet! - There are more viruses There are in ainliter more viruses a literofofcoastal seawater coastal water than than people people on this Earth on Earth. Viruses comprise ~ comprise Viruses 94% of~the 94% ofnucleic-acid-containing particles the nucleic-acid-containing particles. Due to their small size, However, viruses because only of their smallcomprise ~ 5%only size they comprise of ~the biomass 5% of on this earth the biomass. Prokaryotes (e.g. bacteria) Protists Viruses F.Y.I. Protists are any eukaryotic organisms that are not animals, plants or fungi 23 Suttle, Curtis. Nature (2007) (e.g. Amoeba)  Climate change affect spread of human pathogenic diseases Climate change could shift the geographic ranges of 3,100 mammal species and the viruses they carry by 2070 Climate change is increasingly driving new encounters between mammal species, raising the risk of novel disease spread Over the next 50 years, climate change could drive more than 15,000 new cases of mammals transmitting viruses to other mammals 58% of infectious diseases confronted by humanity worldwide have been at some point aggravated by climatic hazards 24 Carlson et al., Nature (2022); Mora et al., Nature Climate Change (2022)  Please download and install the Slido app on all computers you use A virion is: ⓘ Start presenting to display the poll results on this slide. 25 Size of viruses 26  Viruses are small! DO NOT NEED TO KNOW EXACT MEASUREMENTS Very small, cannot be seen with a light microscope Require electron microscopy 100 million polioviruses could fit side by side on the period at the end of this sentence. Range from 20 nanometers (nm) to 1000 nm in length Most viruses studied to date have a size between 20 – 300 nm Giant viruses are about 500 nm in diameter – about the diameter of many bacterial cells 27 Copyright Pearson (2020)  Giant viruses First giant virus was discovered in 2003 and named Mimivirus (for “mimicking microbe”) Mimivirus first seen in its amoebae host but mistaken for a bacterium Large capsid of ~400 nm with protein filaments extending ~ 100 nm from the surface Large DNA genome encoding ~1000 genes (avg. viruses encode a few genes) Giant viruses are also known as Nucleocytoplasmic Large DNA viruses (NLDV) because they are often able to replicate in both the Mimivirus host's cell nucleus and cytoplasm 28  Giant viruses challenge our current view of evolution Giant viruses infect only eukaryotic unicellular hosts such as amoebas, algae and other protists Their genomes are large and very diverse - Giant viruses may have been small viruses that were experts at stealing genes from their host during evolution Hypothesis: Some giant virus genes likely originated from bacteria, archaea, and even other viruses and thus, acquired genes by lateral transfer from bacteria or viruses with an intra-amoebal lifestyle Evolutionary complexity; gene exchange between viruses and Giant viruses have played a significant role in evolution hosts of eukaryotes through gene exchange 29 Aylward, Frank & Mohammad Moniruzzaman, Biomolecules (2022)  Giant viruses have their own viral parasites Virophages: small DNA viruses that replicate only in cells co-infected with a giant virus. Virophages use the viral replication factory established by the giant virus. Virophage associated with mimivirus Sputnik: the first virophage discovered. It replicates only in Mimivirus-infected amoeba cells. Virophages have a parasitic relationship with the co-infecting giant virus. For example, Sputnik reduces Mimivirus replication by ~70%. By interfering with giant viruses, virophages may improve survival of the host. For example, by preventing cell lysis by the giant virus. Giant virus-virophage interactions Rodrigues et al., Encyclopedia of Virology (2021); Aylward, Frank & Mohammad 30 Moniruzzaman, Biomolecules (2022) Are all viruses bad? 31  Most viruses are not pathogenic Biologists estimate that 380 trillion viruses are living on and inside your body right now—10 times the number of bacteria - Some cause illnesses but most coexist with us Viruses play a crucial role in many ecosystems - Viruses help control bacterial populations and influence the evolution and diversity of their host organisms Bacteriophages (Phages), viruses that infect and kill bacteria, can be used as phage therapy to combat bacterial infections in humans! Pride, David. Scientific American (2020); Roossinck, Marilyn. Nature 32 Reviews Microbiology (2011); Hill, Colin. Frontiers for Young Minds (2019)  Gut Bacteriophage and Evolution Research at McGill! Dr. Corinne Maurice Dr. Jesse Shapiro Role of bacteriophages as regulators of the Bacteria and bacteriophage co- active gut microbiota evolution 33  Most viruses are not pathogenic…but some are There are many human diseases caused by viruses (will see some in a later lecture) THIS SLIDE IS NOT ON THE EXAM, DO NOT MEMORIZE 34 Image: Mikael Haggstrom  Please download and install the Slido app on all computers you use Which characteristics of viruses are true? [could have more than one answer] ⓘ Start presenting to display the poll results on this slide. 35  Please download and install the Slido app on all computers you use Your friend had a viral infection and said, “All viruses are bad! The doctor saw the virus under a light microscope and said it was a naked virus, whatever that means. They said it is an RNA virus, which doesn't exist so they must be wrong." Your response? ⓘ Start presenting to display the poll results on this slide. 36  Summary Viruses are important to understand and study for a variety of reasons They are not living, obligate intracellular parasites A virion or virus particle is an extracellular form of a virus - Capsid surrounding nucleic acid (DNA or RNA) = nucleocapsid - Some viruses are enveloped and have glycoproteins Viruses can infect nearly all organisms Size: Small and require electron microscope (20 nm to 1000 nm in length) - Except giant viruses (Nucleocytoplasmic Large DNA viruses) Only infect eukaryotic unicellular hosts Virophages – small DNA viruses that replication only in cells co-infected with a giant virus Not all viruses are bad (ex. Bacteriophages) … but some are! 37