Viral Structure and Replication PDF

BIOM 611G, Medical Microbiology PCOM Georgia INTRODUCTION TO VIROLOGY: VIRAL STRUCTURE AND REPLICATION Valerie E. Cadet, PhD Assistant Dean of Health Equity Integration Professor of Microbiology and Immunol...

BIOM 611G, Medical Microbiology PCOM Georgia INTRODUCTION TO VIROLOGY: VIRAL STRUCTURE AND REPLICATION Valerie E. Cadet, PhD Assistant Dean of Health Equity Integration Professor of Microbiology and Immunology BMS1 & BMS2 Department of Biomedical Sciences January 7, 2025  Required Reading: Murray’s Medical Microbiology, 9th Ed Ch.36 Viral classification, structure and replication LEARNING OBJECTIVES Through the study of this content and recommended reading, the successful student will be able to……. 1. Outline how viral properties enable the classification of different types of viruses. 2. Describe the components of a viral particle and the function of each component as it relates to the viral replication cycle. 3. Describe how properties of different types of viruses influence viral transmission between hosts and viral spread between cells. 4. Compare & contrast the replication cycles of different types of viruses: 1. DNA, +ss RNA, -ss RNA, dsRNA, retroviruses 5. Explain how viral and host factors can influence manifestation of disease 2 DISCOVERY OF VIRUSES… SERENDIPITY AT ITS FINEST Tobacco Mosaic Virus (TMV):  Iwanowski (Russia in 1892) – found that after bacteria are removed by filtration of sap, sap remains infectious (thought it was a bacteria or bacterial product)  Stanley (USA 1935) – crystallized TMV from plant extract  Electron microscopy reveals virus is rod shaped, helical particle 3  DEFINITION AND PROPERTIES OF A VIRUS Virology: scientific study of viruses and the diseases they cause Properties 1. Non-filterable through bacteriological filters 2. Obligate intracellular parasite 3. Cannot make energy or proteins independently of a host cell 4. Contain either DNA or RNA, but not both 5. An infective particle consists of nucleic acid in a protein coat (naked) or surrounded by an envelope (enveloped) 6. An infective particle must self-assemble individual parts rather than reproduce by binary fission or ‘division’ 4 VIRAL STRUCTURE + GENERAL CONCEPTS 5  Outline WHAT ARE THE how viral properties DIFFERENT enable the classification of different types of FEATURES OF viruses. VIRUSES THAT HAVE Describe LENT THEMSELVES components of a viral TO HOW VIRUSES particle and the function of each component as it ARE CLASSIFIED? relates to the viral replication cycle. *Describe how properties of different types of viruses influence viral transmission between hosts and viral spread 6 SCHEMATIC DIAGRAM OF AN INFECTIVE VIRAL PARTICLE  Delivery system  protects against degradation in the environment  contains structures used to bind to host target cells  Payload  contains the genome and enzymes necessary to initiate the first steps in virus replication. 7 FIGURE 32-2 Schaeter’s Mechanisms of Microbial Disease  THE PAYLOAD: DNA OR RNA  DNA viruses  Single or double stranded  Linear or circular  Open or closed ends  Continuous or nicked  RNA viruses  Single or double-stranded  If single, either + or - sense  Linear  May be segmented 8  COMPONENTS OF THE BASIC VIRION  NUCLEIC ACID: DNA or RNA  Core = genome + associated enzymes  CAPSID: protein shell that encloses the nucleic acid (single or double)  Helical, icosahedral or complex  NUCLEOCAPSID: capsid + nucleic acid  The nucleocapsid may be enclosed in lipid bilayer ENVELOPE host cell derived with viral glycoproteins  MATRIX: protein that organizes and maintains virion structure  aka tegument in Herpesviruses  VIRION = structurally complete infective virus particle 9 FIGURE 36-1 Murray’s Medical Microbiology CAPSID SYMMETRY (STRUCTURE) Icosahedral Symmetry Helical Symmetry Adenovirus Ebola virus EXCEPTION TO 2 TYPES OF SYMMETRY: COMPLEX SYMMETRY VIRUSES 1. Poxviruses 2. (dsDNA) Bacteriophages 11 CONSEQUENCE OF NAKED/NON- ENVELOPED CAPSID ON VIRUSES  Protects viral genes from inactivation by Clinical Consequences adverse environmental factors  Survival in the environment enables  Temperature, acid, proteases, detergents, drying, sewage treatment transmission via fomites  Difficult to disinfect contaminated surfaces  Mediate attachment via a viral attachment protein (VAP)  Survival in the GI tract enables  Package, protect and deliver the genome transmission via the fecal – oral route during transmission  Shed in stool  Released via cell lysis  Present in sewage-contaminated water  Responsible for most cases of viral gastroenteritis  Cytopathic  CONSEQUENCE OF ENVELOPE ON VIRUSES  Consists of host-derived lipid bilayer  Embedded viral surface glycoproteins  Facilitate attachment  Mediate viral-cell fusion  Induce neutralizing (protective) antibody which blocks infection  Associated matrix proteins facilitate assembly  Viral infectivity decreased by environmental conditions  Chemical agents/detergents can dissolve lipids  Acid & heat labile  Must stay wet to retain infectivity  Important in determining host cell specificity and sometimes cell penetration (tropism)  Released via budding (may cause cell lysis over time) CONSEQUENCE OF ENVELOPE ON VIRUSES, CONT. Clinical Consequences  Transmitted through droplets & secretions  Respiratory route; blood; organ transplants  Cannot survive in the gastrointestinal tract (usually)  Not transmitted fecal/orally  Need not kill infected cells to spread  Potential for persistence  GENERAL ORDER OF MICROBIAL RESISTANCE AGAINST BIOCIDES AND BIOCIDAL PROCESS IS BASED ON SIZE AND ENVELOPE STATUS, AMONG OTHER FACTORS https://www.researchgate.net/figure/258425493_fig2_Figure-2-General-order- 15 of-resistance-against-biocides-and-biocidal-process-It-should-be [accessed Sep NAMING AND CLASSIFICATION OF VIRUSES  Knowledge of the structural (size and morphology) and genetic (type and structure of nucleic acid) features of a virus provides insight into how the virus replicates, spreads, and causes disease.  Viral names may describe viral characteristics, diseases they are associated with, or even tissue or geographic locale where they were first identified  Viral grouping occurs based on various characteristics  Most consistent classification is by physical and biochemical characteristics, such as size, morphology (e.g., presence or absence of a membrane envelope), type of genome, and means of replication 16 TYPE OF CAPSID + GENOME TYPE 1. Icosahedral, non-enveloped 3. Helical, non-enveloped i. dsDNA i. dsDNA ii. ssDNA ii. ssDNA iii. dsRNA iii. ssRNA iv. +ssRNA 4. Helical, enveloped 2. Icosahedral, enveloped i. +ssRNA i. dsDNA ii. -ssRNA ii. +ssRNA 5. Complex, enveloped i. dsDNA (poxviruses) 20 non-enveloped virus AKA naked capsid  CLASSIFICATION: DNA VIRUSES OF MEDICAL IMPORTANCE DNA viruses associated with human disease are divided into seven families 21 Adapted from: FIGURE 31-5 Schaeter’s Mechanisms of Microbial  CLASSIFICATION: RNA VIRUSES OF MEDICAL IMPORTANCE RNA viruses associated with human disease may be divided into at least 14 22 families Adapted from: FIGURE 31-5 Schaeter’s Mechanisms of Microbial Disease VIRAL REPLICATION 23  6 BASIC STEPS OF VIRAL MULTIPLICATION 1) Attachment 2) Penetration/ entry 3) Uncoating/ release of nucleic acid from capsid 4) Biosynthesis of protein and nucleic acid 5) Assembly 6) Release 24 STEP 1 (ATTACHMENT/ ADSORPTION) DEPENDS ON 2 FACTORS: 1) VIRUSES HAVING THE RIGHT V.A.P. 2) CELLS HAVING THE RIGHT RECEPTOR Viruses have viral attachment proteins (VAPs) that extend away from surface of virion VAPs in enveloped viruses extend through envelope; known as glycoprotein spike proteins STEP 2: PENETRATION/ENTRY VARIES BASED ON IF THERE IS A VIRAL ENVELOPE OR NOT  HOW DO MOST ENVELOPED VIRUSES GAIN ENTRY INTO A HOST CELL? 1. Attachment to cell- surface receptors via attachment protein 2. Penetration of host-cell membrane by fusion protein 3. Fusion of viral envelope and cell membrane 27 SIB Swiss Institute of Bioinformatics, https://viralzone.expasy.org HOW DO NON-ENVELOPED & SOME ENVELOPED VIRUSES GAIN ENTRY INTO A HOST CELL? 28 SIB Swiss Institute of Bioinformatics, https://viralzone.expasy.org  FUSION  SYNCYTIUM FORMATION IN SOME VIRAL INFECTIONS Viral Families Affected o Formed by fusion of infected cells with neighboring cells  leads to formation of multi-nucleated enlarged cells 1. Herpesviridae 2. Paramyxoviridae o Induced by surface expression of viral fusion protein(s) 3. Poxviridae that are fusogenic directly at the host cell membrane 4. Retroviridae o Syncytia can only happen with viruses able to directly 5. Reoviridae fuse at the cellular surface without the need of endocytosis Syncytial formation caused by RSV in cell culture. 29 SIB Swiss Institute of Bioinformatics, https://viralzone.expasy.org (Courtesy of Linda Stannard, University of Cape  STEP 3: UNCOATING/ RELEASE OF NUCLEIC ACID FROM CAPSID DNA viruses: genome must be delivered to nucleus Exception = poxviruses RNA viruses: genome remains in cytoplasm Exception = orthomyxoviruses STEP 4: BIOSYNTHESIS OF PROTEIN AND NUCLEIC ACID (REPLICATION)  Compare & contrast WHAT ARE THE replication cycles of DIFFERENCES different types of BETWEEN HOW viruses VIRUSES WITH DNA DIFFERENT GENOME +ss RNA STRUCTURES -ss RNA REPLICATE? dsRNA retroviruses *Describe how properties of different types of viruses influence viral transmission between hosts and viral spread 32  PROPERTIES OF VIRUSES BASED ON GENOME DNA RNA  Not transient or labile  can persist over time  RNA is labile and transient  Chronic  Replication and transcription  cytoplasm  Latent; immortalizing  Except for orthomyxovirus: influenza  Replication and transcription  nucleus  Encode own polymerases  May exist as separate plasmid-like DNA molecule or integrate into host chromosome  Viral RNA-dependent RNA polymerase  DNA resembles host DNA for transcription and  Except for retroviruses (RNAdep- replication DNApol)  Can use host polymerases  Genome structure and polarity  Require a primer to replicate viral genome determine how viral mRNA is generated  Interacts with host transcription factors and proteins processed  Exception???  Prone to mutation allowing for adaptation to host  Viral gene transcription is temporally regulated  Early and late gene transcription  Variability  quasi-species  Immune escape variants 33 VIRAL POLYMERASES RNA viruses 1. RNA-dependent RNA polymerase (RdRp) 2. RNA-dependent DNA polymerase (RdDp)/ Reverse transcriptase (RT) 3. DNA-dependent DNA polymerase (DdDp) 4. DNA-dependent RNA polymerase (DdRp)  Note  Viral plus-sense RNA can serve as an mRNA and does not require modification for transcription. DNA viruses Many dsDNA viruses do not encode viral polymerase and instead use cellular enzymes in nucleus for viral genome transcription and replication 1. Orthopoxviruses encode DdRp and DdDp 2. Hepadnaviruses encode RdDp/RT 34 BALTIMORE CLASSIFICATION Baltimore classification scheme, most commonly used, was developed by Nobel Prize-winning biologist David Baltimore, early 1970s. Groups viruses according to how mRNA is produced during the replicative cycle of the virus, in addition to differences in morphology and genetics Example Disease - virus (virus Group Characteristics Mode of mRNA Production family) Cold sore - herpes simplex virus I Double-stranded DNA mRNA transcribed directly from DNA template (herpesvirus) DNA converted to double-stranded before RNA II Single-stranded DNA Parvovirus - B19 (parvovirus) transcribed Childhood gastroenteritis - rotavirus III Double-stranded RNA mRNA transcribed from RNA genome (reovirus) Common cold - rhinoviruses IV Single stranded RNA (+) Genome functions as mRNA (pircornavirus) V Single stranded RNA (-) mRNA transcribed from RNA genome Rabies – rabiesvirus (rhabdovirus) Single stranded RNA Reverse transcriptase makes DNA from RNA Human immunodeficiency virus – HIV VI viruses with reverse genome; DNA then incorporated in host genome; (retrovirus) transcriptase mRNA transcribed from incorporated DNA Viral genome is double-stranded DNA, but viral Double stranded DNA DNA is replicated through RNA intermediate; the Hepatitis - Hepatitis B virus 35 VII viruses with reverse RNA serves directly as mRNA & as template to (hepadnavirus) transcriptase  STRATEGIES FOR Group VIRAL 1 REPLICATION 7 Hepadnaviruses (dsDNA-RT virus)  partial dsDNA genomes  ssRNA intermediates that act as mRNA 2  ssRNA intermediates are also converted back into dsDNA genomes by reverse transcriptase, necessary for genome replication 4 5 3 6 36  STEP 5: ASSEMBLY Capsids self-assemble Package genome & core enzymes STEP 6: RELEASE OVERVIEW OF ASSEMBLY & RELEASE Non-Enveloped Viruses Enveloped Viruses 1. Assembly of capsid structure 1. Assembly of capsid or nucleocapsid with genome to 2. Insertion of genome into capsid form core 3. Assembly may occur in 2. Assembly of envelope (modified cytoplasm or nucleus patch of cell membrane depending upon virus family 3. Association of core with membrane 4. Release of virions from cell requires cell lysis (at least 4. Release from cells by budding partially) from a plasma membrane or golgi, RER or nuclear membranes 5. Does not require cell death 39 FACTORS INFLUENCING DISEASE MANIFESTATIO N 40  Explain HOW COME how viral and host SOME PEOPLE factors can GET SICK WHEN influence INFECTED manifestation of disease WHILE OTHERS DON’T? *Describe how properties of different types of viruses influence viral transmission between hosts and viral spread 41 FACTORS WHICH INFLUENCE DISEASE Viral factors Host factors  Transmission determines site of entry  Immune status  Inoculum size influences severity  Compromised versus non-  Tissue tropism determines site of compromised immunity pathology  Prior immunity  Viral virulence factors include  General health of the patient mechanisms to  Nutrition  control host cell protein synthesis   Age evade the immune response   Genetic background directly damage cells 42 ON YOUR OWN TO DO: DRAW AND LABEL THE BASIC VIRION WITH ALL APPLICABLE COMPONENTS Naked Enveloped 44 TO DO: LIST THE DNA AND RNA VIRUS FAMILIES OF MEDICAL IMPORTANCE TO HUMANS DNA Viruses RNA Viruses 45 TO DO: LIST MAJOR VIRUS FAMILIES OF MEDICAL IMPORTANCE TO HUMANS BASED ON THEIR GENOME, CAPSID & ENVELOPE STATUS DNA Viruses RNA Viruses 46 TO DO: LIST THE DNA VIRUS FAMILIES OF MEDICAL IMPORTANCE TO HUMANS ALONG WITH THEIR REPLICATON SCHEMES DNA VIRUS FAMILY REPLICATION and PROTEIN SYNTHESIS EXAMPLE OF VIRUS IN SCHEME FAMILY 1 2 3 4 5 6 7 47  TO DO: LIST THE RNA VIRUS FAMILIES OF MEDICAL IMPORTANCE TO HUMANS ALONG WITH THEIR REPLICATON SCHEMES RNA REPLICATION and EX OF RNA REPLICATION and EX OF VIRUS PROTEIN SYNTHESIS VIRUS IN VIRUS PROTEIN SYNTHESIS VIRUS IN FAMILY SCHEME FAMILY FAMILY SCHEME FAMILY 1 8 2 9 3 10 4 11 5 12 6 13 7 14 48 LTERNATE VIEW: STRATEGIES FOR DNA VIRUS REPLICATION Group VII Group II Group I 49 LTERNATE VIEW: STRATEGIES FOR RNA VIRUS REPLICATIO Group IV N Group V Group III Group VI 50  WHAT ARE THE RULES OF VIRAL REPLICATION (LOCATION IN THE CELL)? 1. DNA viruses replicate in the: 1. DNA virus exception to the rule: 2. RNA viruses replicate in the: 2. RNA virus exception to the rule: 51 EXAMPLE: DESCRIBE NOROVIRUS, A COMMON CAUSE OF VIRAL GASTROENTERITIS Information from CDC: https://www.cdc.gov/vitalsigns/norovirus/index.html  Norovirus outbreaks from contaminated food are common in food service settings.  People infected with norovirus are very contagious.  … they shed billions of tiny viral particles in their stool and vomit…  Norovirus is hard to kill and stays on food, kitchen surfaces, and utensils. It can:  Remain infectious on foods even at freezing temperatures & until heated above 140°F.  Stay on countertops and serving utensils for up to 2 weeks.  Resist many common disinfectants and hand sanitizers.  Illness resolves after ~48 hours with no long-term consequences Each bulleted statement implies what viral property? Ask yourself questions about each one.  Example questions you can make up from the bullets 1. What does the genome of norovirus look like? 2. Why are infected individuals so contagious? 3. What are the viral properties which make norovirus so hard to kill/inactivate? 52 EXAMPLE: DESCRIBE HIV, THE CAUSE OF HUMAN ACQUIRED IMMUNODEFICIENCY SYNDROME  HIV can cause a productive, persistent infection in macrophages; macrophages can shed virus for an extended period of time (days to a couple weeks)  HIV can cause productive infection in activated T cells but latent infection in memory T cells  The host immune response & anti-retroviral therapy both provide selection pressure for the generation of quaisispecies Each bulleted statement implies what viral property? Ask yourself questions about each one.  Example questions you can make up from the bullets 1. What does the genome of HIV look like? 2. What type of infection does this virus cause? 3. What type of polymerase(s) does HIV encode? 53 EXAMPLE: DESCRIBE VARICELLA-ZOSTER VIRUS (VZV), THE ETIOLOGIC AGENT OF CHICKEN POX & ZOSTER?  VZV is transmitted primarily via respiratory droplets, though manifestation of disease involves vesicle formation in the skin  Viral entry and uncoating occur at different sites within a cell  Zoster, but not chickenpox, is an endogenous infection Each bulleted statement implies what viral property? Ask yourself questions about each one. 1. What does the genome of VZV look like? 2. What type of infection(s) does this virus cause? 3. Why is zoster, but not chickenpox, caused by an endogenous infection? 54 ADDITIONAL THOUGHT QUESTIONS 1. What type(s) of viruses have genomes that are “infectious nucleic acids”?  What do these genomes look like? 2. Why does orthomyxovirus replicate in the nucleus?  What does the genome of these viruses look like?  What kind of polymerases do they encode? 3. Why do poxviruses replicate in the cytoplasm?  What does the genome of these viruses look like?  What kind of polymerases do they encode? 55