Chapter 13: Viruses Structure - PDF

11/11/24 Tobacco mosaic virus (TEM) discovered in 1892 Announcements...

11/11/24 Tobacco mosaic virus (TEM) discovered in 1892 Announcements by Dimitri Iwanowski Ch 13 – Tortura Ch 6 – OpenStax Viral Structure and Lab 06 – Epidemiology Replication Cycle Ø No pre-lab Ø Post-lab due Sunday Vocab/Reading quiz – due Tuesday Exam 3 – Wednesday 11/13 https://www.sciencesource.com/archive/Tobacco-Mosaic-Virus--TEM--SS2304521.html 1 2 Major concepts Is it a virus or is it a virion? Structure and classification of viruses Virions are complete, infectious viral particles found extracellularly (non-living) Culturing viruses Ranges and host-specificity Viruses are actively replicating viral particles inside host cells (alive?) Replication cycles (including specific steps of cycles) Virion Disease outcomes Virus Vaccination Emerging pathogens and dangers of a naive population Host cell Host cell Benefits 3 4 Virions are most ubiquitous entity on earth Viruses infect extremophiles Infect all forms of life on earth (prokaryotes & eukaryotes) Found in every environment Ø Many likely not discovered yet Ø Ex: Humans have over 140k viral “species” in gut (mostly phage) Highly adapted at causing infection Ø Often highly host-specific (due to receptor-binding) Ø Unique adaptations to their particular hosts Ø Many manipulate hosts for transmission Treatments often difficult due to infection cycle and lack of targets 5 6 1  11/11/24 Viruses are very Viruses tend to be host-specific small Streptococcus cell (1 μm) Each kingdom has their own types of viruses Ø Ex: bacteriophage (phage) - infect bacteria; Bacteriophage mycophage - infect fungi, (65nm) Discovered HSV I (150nm) Ø Phages do not infect plants, plant viruses do not infect because could not be filtered mammals, etc. Assumed to be a Host cell binding receptors used are different between Polio virus toxin = “virus” species Influenza (30nm) virus (100nm) Viruses are even tissue specific in animals RBC (6 μm) 7 8 Viruses are acellular pathogens Viruses require host to replicate Frozen virus and Require host to be studied cells for future use Origins unknown, but considered non-living (sometimes) Ø Cell/tissue culture - immortal cells Ø No cellular structures and cell nutrients Ø No machinery for protein synthesis Ø Animal culture requires living hosts Ø No enzymes for metabolic processes (sometimes killing host) Ø Kept as frozen stocks Break fundamental rules in biology Picture credit: John Nichols, HKU -80º C Ø Nucleic acid make-up Ø Dogma of protein synthesis Obligate intracellular parasite Ø None are free-living Ø Reproduce inside proper host cells Coronavirus particles binding to Liquid Ø “Dies” in external environment host cell membrane nitrogen Nutrients in media feed host cells 9 10 Viral work requires special precautions Viral classification status… it’s complicated Culturing viruses is important Ø Identification occurs through isolation International Committee on Taxonomy of Viruses (ICTV) Ø Vaccines can be produced Ø Responsible for classifying viruses Ø Understand structure, biology to understand infection “Species” criteria include genetic sequence similarities, Many viral disease have Biosafety levels 1-4 capsid structure, enveloped/naked, host range, pathogenicity no cures Ø Still use strains to refer to viruses Ø High level of Ø Ex: HIV group M has strains A-J and K (with substrains) protection required Ø Once exposed, few Baltimore classification based on type of genome (in core) cures exist Ø Nucleic acid, strandedness, sense, method of replication Also used for dangerous pathogens (e.g., antibiotic resistant microbes) 11 12 2  11/11/24 Virions are nucleic acid surrounded by proteins Capsids can be icosahedral, helical, or complex Genome Genome Genome Capsid Constructed of repeating molecular units Ø External capsid Capsid Capsid Filamentous shaped virus Ø Nucleic acid core External structures: Ø Capsid (shell) made of proteins Ø Protein spikes (some viruses) Ø Envelope made from host plasma membrane (some viruses) Core Ø Nucleic acid (DNA or RNA, ss or ds) T4 phage infect E. coli https://www.khanacademy.org/science/high-school-biology/hs-human-body-systems/hs-the-immune-system/a/intro-to-viruses Ø Matrix proteins (some viruses) Ø Enzymes (some viruses) Capsomeres are protein subunits that make up capsids 13 14 Some virions have envelope surrounding capsid Naked nucleocapsid Enveloped virus envelope Most bacteriophage do not have envelopes A Naked viruses have nucleocapsid Capsid B Envelope of lipids, proteins, and/or Nucleic carbohydrates acid C Ø Origin partly viral and partly host D Many envelopes have “spikes” or glycoproteins Ø Used for attachment Ø Antigenic capsid 15 16 Bacteriophage are bacterial viruses Bacteriophage inject genome into bacterial host Infection result in pathogenic consequences to bacterial host Very host specific Can cause lytic (destructive) or lysogenic Bacteriophage alone, more common than (incorporative) infections all lifeforms combined! https://www.wired.com/2015/09/menagerie-viruses-lurks-microbial-dna/ 17 18 3  11/11/24 We are home to millions of bacteriphage Animal viruses come in a variety of flavors Bacteriophage have a protective role against pathogenic bacteria Control bacterial growth Externally proteinaceous (Capsid) Sometimes enveloped Internally genome (RNA Our genome has tons of viral DNA or DNA) 19 20 Naked, helical Naked, icosahedral with fibers (glycoproteins or spikes) Ex: tobacco mosaic virus Ex: adenovirus Nucleic acid Capsid Capsid Fiber (spike, glycoprotein) 21 22 Envelope Enveloped, filamentous Viruses of clinical importance for humans Ex: influenza virus, segmented genome (BSL - 2) Spike Ø Herpesviridae (HSV 1, 2, EBV, chicken pox, Kaposi’s sarcoma) Ø Flaviviridae (Dengue, West Nile, Yellow fever) Ø Hepadoniviridae (Hep B) Ø Paramyxoviridae (measles, mumps) (BSL – 2 or 3) Orthomyxoviridae (influenza A) (BSL – 3) Ø Coronaviridae (SARS, CoV19, MERS) Ø Papoviridae (HPV) Ø Retroviridae (HIV) (BSL – 4) Filoviridae (Ebola, Marburg), Arenavirus (Lassa Nucleocapsid fever), and several hemorrhagic fevers (RNA and proteins) 23 24 4  11/11/24 Viruses replicate to Viruses have infection cycles (not life cycles) high numbers Infection cycle has various steps Entry Ø Attach via specific receptors Viral attachment and entry Ø Fusion to membrane Ø Endocytosis Viruses only infect requires receptor-ligand tissues for which they binding have receptor affinity Replication Eclipse Interactions between cell period Ø DNA to nucleus surface molecules and Ø RNA to ribosomes glycoprotein ligands Exit Single virion can produce Ø Budding (extrusion in phages) thousands of new virions Ø Lysis 25 26 Viral characteristics dictate replication cycle The viral core directs replication Particle size restricts genome size Ø 4 genes - hundreds of genes Genes code for enzymes involved in Ø Replicating viral genome Ø Synthesis of capsid proteins Ø Packaging mature virus Some viruses carry enzymes in core Ø Polymerase – synthesize genome Ø Replicase – copy RNA Ø Reverse transcriptase – synthesize DNA from RNA What does the replication cycle of a naked, + sense RNA virus look like? 27 28 Genome sense directs replication Capsid covering, or lack of, directs entry and exit Viral strand sense dictates replication step + strand (sense) DNA and RNA are translatable strands Naked capsids attach and inject DNA - strand (sense) DNA and RNA are template Naked virions generally cause lysis to host cells Negative sense nucleic acid must be replicated into positive sense, and THEN, can be transcribed or translated Enveloped viruses bind to receptors on cell membrane Ø Envelope can merge with cell membrane capsid Positive stranded nucleic acid can be readily transcribed centers and translated Or Ø Whole virion phagocytosed (endocytosis) Retroviruses begin at ribosomes and then move to nucleus Enveloped virions acquire envelope from host cell membrane Enzymes for replication coded for by viral genome 29 30 5  11/11/24 Viruses have multiple steps from entry to exit Attachment – entry of particle to host cell by receptor- ligand interactions Penetration – engulfed by cell vacuole/vesicles Uncoating – vacuole/vesicle dissolve envelope & capsid Replication – RNA viruses replicate in cytoplasm/DNA goes to nucleus using host machinery Assembly – structural proteins and genome encased by capsid, spikes sent to membrane Release – viruses exit by cell lysis or budding with cell membrane components https://www.youtube.com/watch?v=D9OtJU3F6eQ&t=9s 31 32 RNA viruses replicate in the cytoplasm Host-specificity determines host range 1) Receptor-mediated Attachment 1 endocytosis restricts host range (specificity) Penetration Attachment necessary for infection 2 Uncoating Entry mediated through receptor-ligand binding 3 Ø Viral proteins must bind host proteins 4 4) RNA viruses replicate in Synthesis cytoplasm while DNA Incorrect ligand to receptor inhibits infection viruses replicate in nucleus Ø Virus will not replicate in host cell and will “die” Assembly 5 Tissue-specificity Release Ø Ex: Influenza A - upper respiratory infections 6 mild to severe 6) Viruses exit by killing cell or budding from it…or Host cell becomes Ø Lower respiratory more severe could remain integrated virus making factory 33 34 Each of our cells express a lot of antigens Example: Entry and specificity of SARS-CoV-2 What antigens do these cells produce? Spike protein uses ACE-2 protein for receptor binding What antibodies do they stimulate? ACE-2 is digestive enzyme Ø Modulates activity of ANG II (pro-inflammatory and BP Individual 1 Individual 2 Individual 3 Individual 4 increasing molecule) Present on epithelial tissue in respiratory tract, lungs, alveoli, heart, blood vessels, kidneys, liver, gastrointestinal tissue A B AB O Viral disease results from Ø Infection of cells Spike proteins Ø Inhibition of ACE2 function ACE-2 expression varies by individual 35 36 6  11/11/24 Example: HIV CCR5-delta 32 mutation Viral replications commonly result in mutants Virus uses CD4 and CCR5 co-receptors to gain entry into macrophages and other WBCs Lack of cell cycle checks produces many mutants During assembly, viral encapsulation can go wrong Ø Extra genome Ø Not enough genome Ø Wrong genome 4 The more virus circulates, the more strains that can result 5 Production of inert and more virulent strains 37 38 CPE and lysis using GFP-tagged Viral exit has different consequences for host primate cells infected with herpes Lytic cycles Ø Virus kills (lyses) host cell as they leave Ø Cause cytopathic effects (CPE) Ø Commonly with naked viruses Normal cells Latency cycles (lysogeny for phage) Ø Virus remains dormant in cell, unintegrated Ø Proviruses, integrated into genome Ø ERVs, endogenous retroviruses, proviruses passed down Cell lysing through evolution Round, shrunken cells HIV becomes provirus 39 40 Viral latency can have side effects HSV-1 lytic phase Intermittent re-activation Ø Herpesviruses – Varicella HSV cause latent infections zoster reactivates as shingles Ø HSV-1, HSV-2, Varicella zoster, EBV, cytomegalovirus, HHV 6, HHV7, KSHV-8 Transformation of host cell Ø Oncoviruses have oncogenic properties Ø Ex: HPV, EBV, KSHV-8 48 hrs post-infection Ø HBV (hep B) 41 42 7  11/11/24 Viral latency can result in cancer Why does latent VZV reappear as shingles? Ellerman and Bang discovered chicken leukemia could be “transferred” with viral infection (1908) Varicella was a common childhood disease Bishop and Varmus proved viruses carry oncogenes (1989) Acquired through aerosols, physical contact with blisters fluid Some viruses encode promoters that activate oncogenes Immune system controls viral replication Oncoviruses integrate genetic material into host and virus goes latent inside nucleus Ø Ex: Herpesviridae, Papillomaviridae, Hepadnaviridae Encounters with virus maintained immunity EBV, HPV, HBV, HTLV-1 and 2 (human T cell leukemia viruses) What changed? 43 44 Proto-oncogene 45 46 HIV goes latent and becomes a provirus Dip due to proliferation of leukocytes Virus continues to kill CD4 cells No viable immune system https://www.youtube.com/watch?v=-M3L_Kykl6w 47 48 8  11/11/24 Transmission varies by virus Virulence can vary tremendously Direct Some viruses are virulent (severe) while others are mild Ø Touch/sexual contact Ø Depending on virus and on host Ø Droplet Ø Ex: Herpes B – mild in monkeys, Adenovirus is mild virus lethal to humans Indirect Ø Airborne Infections can be acute Ø Vehicle – water, soil, fomite or chronic Rabies virus is highly Ø Vector-borne Ø Severe and fast virulent Ø Fecal-oral acting Ø Mild and long-lasting Viral “life span” varies from minutes to days and type of substrate 49 50 Virus infections generally have one of 2 outcomes Viral infections promote transmission Ø Host-specificity - mammals Ø Virus enters PNS through muscles, infects CNS, hidden Host can control infection (natural resistance) or succumb from WBCs (death) Ø Virus interferes with cell-cell communication Ø Virus changes brain chemistry (and behavior!) irrevocably Ø Virus replicates in salivary glands Few antivirals available once infected Fast-replicating viruses are dangerous (virulent) Ø Innate system can’t destroy pathogen Rabies virus Ø Adaptive system cannot work fast enough How do we prevent high mortality in our population? 51 52 Vaccination protects individuals Vaccination protects the human population Naïve immune systems are dangerous because no Vaccines allowed eradication of protection smallpox (Edward Jenner) Vaccines (immunization) provides immunity through Why controversies with memory (adaptive immunity) vaccinations? Population vaccination protects via herd immunity How serious are side-effects? https://www.historyofvaccines.org/content/smallpox-two-boys Ø If majority of people immune, transmission inhibited Ø No vaccination creates naïve, susceptible population Generally, vaccine risks out- weighs disease effect to Immunity protection ranges from months (covid), years individual and population (tetanus), to lifetime (measles) 53 54 9  11/11/24 Emerging pathogens…or are they? Why is flu so dangerous? May be new, but likely re-emerging (zika) or just new to Structure: human population (HIV, SARS) Ø RNA genome Ø Segmented genome (8 segments) Zoonotics – pathogens “jump” from animal to human Ø Hemagglutinin (18) & neuraminidase (11) for population or vice versa Ø Rabies, toxoplasma, anthrax, trichinosis (viral and entry & exit non-viral) Ø Viral examples: Behavior SARS-CoV-2 – bats? Ø Re-assortment in pigs (human and bird virions) HIV – from primates Ebola – from primates West Nile – from birds Direct transmission human-human Flu (A) – pigs/birds Vaccine helps and important, but not 100% full-proof https://timedotcom.files.wordpress.com/2014/10/128624230-copy.jpg?w=720&quality=85 http://www.revolutionhealth.org/wp-content/uploads/2013/09/electron-micrograph-of-influenza-flu-virus.gif 55 56 Hemagglutinin (entry) and neuraminidase (exit) 1918-1919 flu 20-33% worlds population Segmented genome infected 50 million died (~16 million killed Re-assortment in WWI) Covid-19 has killed more Americans, but population size much smaller in 1919 57 58 But viruses are not all bad… Junction Epidermolysis Bullosa (JEB) Alteration of genes for therapeutic purposes Ø Viral vectors replace bad gene with good gene Mutation in genes involved in connective tissue of skin Ø Lack adhesion proteins Ethical questions about manipulation of embryos Ø JEB suffers have skin layers move independently and “modifying” human lineages Ø Develop wounds, blisters Ø Can lead to cancer Minor success with debilitating diseases How can viral gene therapy help? Ø Junctional epidermolysis bullosa (JEB) 59 60 10  11/11/24 Skin cells infected with virus cures JEB Blistered skin Skin stem cells from patient extracted New elastic skin Transduction of stem cells with modified virus containing functional gene Skin grown by cloning cells, then grafted onto affected areas Blister-free skin New skin growth maintained by low number of stem Affected where biopsy taken cells (with inserted viral vector) areas – loss of epidermis Nature: doi:10.1038/nature24487 61 62 11