Virus Structure PDF

Introduction to Virus Structure BVetMed1 [email protected] Learning Outcomes (LO) 1. Describe the basic structure of naked and enveloped viruses 2. Discuss the functions of the structural and non structural viral proteins 3. Appreciated how virus structure impacts on their biology Virus Structure Le...

Introduction to Virus Structure BVetMed1 [email protected] Learning Outcomes (LO) 1. Describe the basic structure of naked and enveloped viruses 2. Discuss the functions of the structural and non structural viral proteins 3. Appreciated how virus structure impacts on their biology Virus Structure Lecture Outline Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Virus structure (LO 1) Genome composition (LO 1, LO 3) Capsid structure (LO 1, LO 3) Properties of enveloped and non enveloped viruses (LO 1, LO 3) Functions of structural and non structural proteins (LO 2) Virus Structure What is a Virus? Obligate Intracellular Parasite Needs a host cell to replicate Lacks organelles No nucleus, mitochondria, ribosomes Extremely small (filterable agents) 1. Bovine calicivirus From Stewart McNulty at Veterinary Sciences, Queen's University, Belfast. Range from 18 230 nm Need an electron microscope to visualise ~ sample -o stain metal oh may stars outside of viable remain virus. : outside host. need well to. provide Virus Structure Virus Size Virus Structure EM of a HIV- Infected T cell Note the several hundred virus particles (shown in green) leaving the T cell Size T lymphocyte 10 µm Virus 100 nm Virus Structure Mammalian Virus Families mame)Viridae (family g.. e Reoviridae Further reading: Virology: Principles and Application by Carter and Saunders 2nd Edition Section 1.3 (page 4 -7) Virus Structure Structure of Naked (un-enveloped) Virus Viral Nucleic Acid Capsid Viral Enzymes Virus Structure Enveloped Viruses Virus envelope Host derived lipid bilayer Virus-encoded glycoproteins; Often form spikes Protrude from the virus surface Viral Nucleic Acid Capsid Viral Enzymes Lipid Bilayer # Viral Envelope Protein. glycoprotec Virus Structure Virus Structure Nature of the viral genome Genome composition Genome structure Structure and symmetry of the viral capsid Presence or absence of an envelope How this impacts the biology of viruses Virus Structure Nature of Viral Genome Genome composition > - farly Some DNA viruses can be circular % - : cames y me for Some ds and ss RNA viruses have genomes that are segmented b ↓ chances of degradation Virus Structure Genome composition Viruses with a DNA Genome ds DNA viruses ss DNA viruses Poxviridae Asfarviridae Herpesviridae Papillomaviridae Adenoviridae Papovaviridae (circular and supercoiled) Hepadnaviridae (partially ds circular and reverse transcribing) Parvoviridae Circoviridae (circular) All monopartite (all viral genes on a single segment) Mostly double stranded (except parvo and circo) 5's' Few are circular -b - structure complementary eg Little diversity in structure. end to adopt nicular structure. Viruses with an RNA Genome Virus Structure Genome composition Double stranded RNA viruses Csegmented Single stranded genome +ve ss RNA -ve ss RNA. Non segmented Segmented Reoviridae (10 -18 segments) Retroviridae (diploid and reverse transcribing) Paramyxoviridae Orthomyxoviridae (6-8 segments) Birnaviridae (2 segments) Arteriviridae Rhabdoviridae Bunyaviridae (3 segments) Picornaviridae Filoviridae Arenaviridae (2 segments) Caliciviridae Bornoviridae Coronaviridae Togaviridae Flaviviridae Mostly single stranded (except Reo and Birna) All have linear genomes Can have more than one segment Segments of Reoviridae and Orthomyxoviridae code for single genes RNA Viruses Virus Structure Genome composition Need a RNA polymerase to copy their RNA genome No equivalent enzyme in the host RNA dependent RNA polymerase (RdRp) RNA polymerases are error prone No proof reading capability Any errors made are not corrected and may change amino acid sequence prof reading submit. absent is Consequence of this RNA viruses are more variable Within a species of virus are more subtypes/serotypes => virus will Often zoonotic (have the capacity to jump from animals to humans) Can evolve rapidly if need be milanot RNA viruses can more readily adapt to new environment Segmentation of RNA viruses Allows virus to increase its diversity very rapidly (reassortment) more transmissible ↓ sen become , adaptable domian Virus Structure Reassortment of Segmented RNA viruses Influenza Genome composition RNA viruses that have a segmented genome can reassort Allow mixing of genes during replication Requires simultaneous infection of different strains of virus that have segmented genomes E.g. Influenza, Bluetongue and rotavirus Bluetongue virus Virus Structure Reassortment allows virus to increase its diversity very rapidly Genome composition Infection of a cell with two strains of the same viruses During replication the segments can Progeny virus may differ from the parents If these are infectious they may allow introduction of new genes - problem Immunity : to epidemic me gene Virus Structure PROMED Reports Nov 2019 Virus Ebola virus Genome composition No of reports in the week ending 13th Nov Filoviridae 3 Rift Valley Fever Bunyaviridae African Swine Fever Asfarviridae Rabies virus Two DNA viruses All other viruses are RNA viruses! Virus Family DNA 3 3 Rhabdoviridae 3 Flaviviridae 2 Coronaviridae 1 West Nile Virus Flaviviridae 1 Dengue virus Flaviviridae 1 Yellow Fever virus Mers-CoV Bluetongue Virus Reoviridae 1 Polio virus Picornaviridae 1 Foot and mouth disease virus Picornaviridae 1 Crimean-Congo Haemorrhagic Disease virus Bunyaviridae 1 Chikungunya virus Togaviridae 1 Eastern Equine Encephalitis virus Togaviridae 1 Lassa fever virus Arenaviridae 1 Zika virus Flaviviridae 1 Paramyxoviridae 1 Canine distemper virus Bagaza virus Equine Herpes virus Flavivirus Herpesviridae DNA 1 1 Virus Structure Genome composition Genome Composition of a Virus affects its Biological Properties DNA viruses are more stable, show very little variation RNA viruses are more variable RNA polymerase is error prone and has no proof reading Can adapt easily to new environments (jump species/zoonotic) Some RNA viruses are segmented and so can reassort or swap genes E.g Influenza and Blue tongue virus Virus Structure Genome composition Capsid structure Capsid Structure All viruses have a protein capsid Encloses the nucleic acid ① Paramyxovirus Three Capsid types Q Icosahedral 8 Helical ① Complex Further reading: Virology: Principles and Application by Carter and Saunders 2nd Edition. Section 3.4 ① Adenovirus ③ Poxvirus Virus Structure Genome composition Capsid structure Icosahedral Capsid Regular structure, strong and compact Twelve vertices 20 triangular sides (facets) (5, 3 and 2 symmetry) Composed of capsomers Most do not have an envelope Adenovirus Capsomers Basic structural building block of the capsid Repeating protein units Can be either Penton capsomers 15 individual proteins Hexon capsomers 16 individual. protes ↓ ↑ fill up spaces of vertices on : Insahedral must have between penton capsomers size i always - virus ↑ as => smallest e. g. 12 capsid penion capsomers ones have Parrovirus penion capsomers just ↓ sit & gives com E robust - nature stable strong structure Virus Structure Parvovirus A Non-Enveloped Icosahedral Viruses Parvoviridae Genome composition 18-26 nm in diameter. The capsid consists of 12 capsomers (T=1 symmetry) 60 copies three proteins (predominantly VP2). Capsid structure Extremely stable structure Parvoviruses can survive in the environment for months Virus Structure Genome composition Capsid structure Helical Capsids Single capsid protein are arranged in a genome Structural unit is one capsid protein All animal viruses with helical symmetry are enveloped Virus Structure Enveloped Helical Capsids Paramyxoviridae Genome composition Capsid structure · irregular shape Helical nucleocapsid containing single-stranded RNA Roughly spherical (about 200nm in diameter) Can be much larger and more pleomorphic. more Examples: Rinderpest virus, Canine distemper virus, bovine parainfluenza virus 3 Approx 180 nm long and 75 nm wide Rhabdoviridae Bullet shaped virion Spike-like projections on surface (G) Nucleoprotein (N) encases the RNA genome Example: Rabies Virus Structure Genome composition Capsid structure Complex Capsid Some viruses have capsid structures that are more complex Neither helical or icosahedral structure Asymmetrical shape complex virus e Bacteriophage: Viruses that infect bacteria Icosahedral head Helical tail Poxvirus Virus Structure Pox Viruses Large, enveloped, ds DNA viruses No capsid symmetry (asymmetric) Brick-shaped or ovoid virion, 220-450nm long and 140-260nm wide. Genome composition · Capsid structure dumbell shape Examples: Smallpox, Mouse pox, Sheep pox (Orf), goat pox. Lumpy skin disease virus (cattle) Orf virus in sheep Genome is enclosed in a core with a dumbbell shape surrounded by a protein capsule. Virus Structure (bul is derived Unenveloped (naked) and Enveloped viruses - , u > - Genome composition receptor enter that allow well Capsid structure Properties of enveloped and non-enveloped viruses Naked viruses Have an icosahedral capsid Adenovirus (icosahedral virus) Enveloped viruses viruses Few have an icosahedral capsid All viruses with a helical capsid are enveloped Mammalian complex viruses are enveloped (pox) Herpes virus (icosahedral virus) Measles virus (helical capsid) Poxvirus (complex capsid) virus to Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Characteristics of Enveloped Viruses More pleomorphic (not a regular shape) Present on All viruses with helical symmetry Minority of icosahedral viruses Viral envelope contains host derived lipid bilayer as well as embedded viral glycoproteins Viral proteins contain receptors needed for virus entry (for naked viruses these are found on the capsid) Virus Structure Enveloped vs Unenveloped (Naked) Viruses Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Enveloped virus (HIV) being released by budding from an infected cell Enveloped viruses acquire envelope as they bud through the host cell membrane (except poxvirus which exits by direct fusion) IKell l host a o Un-enveloped virus (Hantavirus) release from infected cells London School of Hygiene and Tropical Medicine Naked viruses are released by lysis of the infected cell Call hyses) Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Biological Properties of Enveloped Viruses More fragile that viruses with just a capsid More easily destroyed by : Kepel blayer 1 Detergents Disinfectants Outside environment of envelop If the envelope is destroyed, then the virus is not infectious Destroys the receptors needed for entry Virus Structure Genome composition Differences in the Biological Properties of Enveloped and Unenveloped Viruses Unenveloped viruses Components Protein Capsid Lipids; viral glycoproteins and protein capsid Properties Environmentally stable to Temperature Drying out pH Detergents Proteases Environmentally labile destroyed by Heat Drying pH (Acid) Detergents Consequences Can be easily spread Not easily spread (affects mode of transmission- requires large droplets, secretions, transplants/transfusions) Can dry out and retain infectivity Must stay wet Can survive adverse conditions in the gut Less likely to survive in the gastrointestinal tract More resistant to detergents - For decontamination, need to make sure that appropriate detergent is used More easily destroyed by detergents Many lyse cell to release; Therefore has to kill the cell. Released by budding: Does not need to kill the cell to spread; Can cause persistent infections Capsid structure Properties of enveloped and non-enveloped viruses Enveloped viruses Virus Structure Biological Properties of Viruses Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Can vary depending on Whether the virus has an envelope Structure and composition of its genomic material Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Viral Proteins Structural proteins Capsid proteins Envelope proteins Matrix protein (layer inside the envelope and outside capsid present in some viruses) Virion-associated enzymes Non Structural proteins Proteins that are not structural components of the virus Often enzymes involved in the replication cycle (but some enzymes can be structural) Also some viruses encode regulatory proteins, oncoproteins, etc. Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Function of the Virus Capsid Proteins Structural Component of the virus capsid Protect the viral nucleic acid and deliver the viral nucleic acid to the cell Capsids of naked viruses contain receptors that attach to the host membrane to allow entry Assembly- capsid proteins self assemble into capsids during replication Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Virus Envelope Proteins Structural proteins of the virus, often glycosylated Embedded in a host-derived lipid bilayer Contain receptors that allows the virus to attach to a permissive host cell receptor and then enter the host cell Are targets of the host immune response (humoral and cellular) Antibodies will recognise these surface exposed viral proteins Antibodies elicited may be protective (neutralising) Interact with the capsid during virus assembly Influenza Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Viral Matrix Protein Connects the viral envelope with the virus capsid ladditional layer Plays a crucial role in virus assembly interacting with the virus nucleocapsid and viral envelope Only found in some viruses Paramyxoviruses, Orthomyxoviruses, Herpesvirus, Retroviruses Influenza Matrix M1 protein Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Enzymes that are structural proteins Some RNA viruses have to carry their RNA polymerase as a structural protein Needed to replicate their genome on infection E.g. all the ve sense RNA viruses - Influenza RNA dependent RNA polymerase consists of three subunits (PA, PB1, PB2) Part of the nucleocapsid carry polymerase complex of the end of each a - segment - t 8 segments. Virus Structure Genome composition Non Structural Viral Proteins Are not structural components of the virus particle Made in the virus-infected cell following infection: Often enzymes involved in viral replication cycle Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Proteases Helicases Polymerase (can be a structural protein!) Protein primers for nucleic acid replication Can be proteins that help the virus avoid the host immune response Targets of the host cellular response (T cell epitopes) : Internal : X recognised by antibodies Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Summary: How Virus Structure Impacts its Biology Virus Structure Feature Impact on Biology RNA virus (error prone RNA polymerase) Increase diversity: Antigenic variation RNA segmented genomes Increased variation (by reassortment). Naked icosahedral viruses Stable in the environment Easily transmitted Stable in the gut Acute infections Enveloped viruses Less stable in the environment Often need direct contact for transmission May cause persistent infections Summary: One Health Relevance Significance to animal health and welfare Understanding how the composition of viruses (type of virus genome and capsid structure) influences their biological properties. This can inform infection control and biosecurity procedures and can help provide better treatment and prevention of viral diseases Significance to public health Understanding that some viruses are zoonotic and so may pose a danger to human health. Some viruses depending on their genetic makeup may be more likely to evolve rapidly and cross the species barrier effectively. Significance to ecosystem health Understanding the biological properties of viruses and how some viruses may be more stable in the environment can help improve infection control and biosecurity measures and so lead to less environmental contamination Virus Structure Genome composition Capsid structure Properties of enveloped and non-enveloped viruses Function of structural and non structural proteins Learning Outcomes Describe the basic structure of naked and enveloped viruses Discuss the functions of the structural and non structural viral proteins Appreciated how virus structure impacts on their biology Virus Structure Lecture Recommended Reading Fenner s Veterinary Virology (MacLachlan and Dubovi): Chapters 1 and 2 Veterinary Virology (Murphy, Gibbs, Howrzinek and Studdert); Chapter 1 Learning Outcomes 1. Describe the basic structure of naked and enveloped viruses 2. Discuss the function of viral structure and non structural proteins 3. Appreciate how virus structure impacts on their biology Viruses cause many important diseases in humans and animals. Often called obligate intracellular parasites. Viruses cannot replicate outside living cells. Dependent on the metabolic and genetic functions of the host (nucleus, ribosomes/mitochondria) Depend on host to supply habitat and raw materials (i.e. amino acids and nucleotides) Do not have the capacity to produce or store energy i.e. metabolically inert Some viruses can survive for prolonged periods in the external environment. (Some small unenveloped viruses with stable icosahedral structure) Virus structure is not cellular. Lack organelles no internal membranes or cytoplasm Viral components are made using the organelles from a host cell only Some use cellular processes in replication of genome as well as well as to synthesise viral proteins Therefore, depends on host cell for Building blocks (i.e. amino acids and nucleotides) Protein synthesis machinery (i.e. ribosomes) Energy (ATP/mitochondria) Note: Viruses do NOT divide. When a virus enters a cell it disassembles and ceases to exist as an entity. New progeny virus are made by assembly of viral proteins and nucleic acid Viruses attach and enter a permissive host cell. They may hijack the host cell processes to copy their genome and synthesise new viral proteins. Then new particles are made by self assembly. Some viruses have to code for essential enzymes involved in their replication cycle Enzymes that the host cannot provide e.g. o RNA dependent RNA polymerase As RNA viruses have their genomic information in the form of RNA, they need an enzyme to copy this (all other organisms make RNA from DNA) o Reverse transcriptase Viruses that copy RNA to make DNA e.g. Retroviruses Viruses are extremely diverse in size Virus particles can only be visualised using an electron microscope which uses beams of highly energetic electrons to exam the surface of virus Thin sectioning of virus infected cells/tissue (limits resolution of EM to 5-7.5 nm) Negative staining of cell free virions (obtained from clinical samples) with electron dense compounds such as uranyl acetate or potassium phosphotungstate Note that some of the largest viruses are larger than the smallest bacteria Size of viruses range from: Extremely small Picornaviridae (28-30 nm); Parvoviridae (18-26 nm) Largest mammalian viruses: Poxviridae (170-200 x 300-450 nm); Filoviridae (80 x 790-14000 nm) Viruses are also diverse in shape Some spherical with smooth surface (Parvoviridae, Picornavirdae) Irregular roughly spherical (Paramyxoviridae) Some have projections (Orthomyxoviridae) (e.g. spike proteins on Influenza) Adenoviruses have fibres projecting from the corners Some have an irregular shape (Rhabdoviruses have typical bullet shape) Virus Composition A virion is a single complete virus particle. It is composed of: virus nucleic acid, surrounded by a viral capsid. This structure may also have an envelope. Nature of the Viral Nucleic Acid: Viral nucleic acid can be composed of either DNA or RNA DNA viruses can be classified depending on the structure of their DNA o Double stranded (ds) DNA (e.g. Papillomavirueses) o Single stranded (ss) DNA viruses (e.g. Parvoviruses) Key facts Most DNA viruses are double stranded (except parvo and circovirdae) Some ds DNA genomes can be circular. All DNA viruses are monopartite (all genome information on a single piece of DNA) DNA viruses replicate in the nucleus (except poxviruses (codes for all replication enzymes therefore can remain in the cytoplasm) Genomes can be larger; Herpes/poxviruses RNA viruses o ds RNA viruses (segmented) (eg Reoviruses) o ss RNA viruses (are further classified depending on the polarity of the ss RNA) Positive sense ss RNA viruses. A (acts as mRNA and so can be translated directly to protein). This circumvents the earliest stage in replication): Genomic RNA is infectious. Small genome size as limited by the fragility of the RNA as there is a tendency for ssRNA to break. Negatively Sense ss RNA viruses. (needs to synthesise a +ve sense mRNA before viral proteins can be translated). Not infectious as purified RNA. More diverse than +ve ssRNA viruses. May have segmented genomes e.g. influenza Key facts Some RNA viruses are monopartite Some RNA viruses are segmented (have more than one piece of genomic material o All ds RNA viruses are segmented o Some segmented viruses Have a single gene on each segment (influenza) Have 2 segments one coding for structural proteins the other for non structural proteins o Segmentation allows the viruses to increase their diversity by allowing the possibility of new gene combinations hence aiding rapid evolution. o RNA viruses replicate in the cytoplasm with exception of o Influenza (needs RNA splicing enzymes that are found in the nucleus) o Retroviruses (need to integrate into the host chromosome as part of their life cycle) Capsid symmetry The viral capsid is a protein layer that encloses and protects the nucleic acid. Its function is to deliver the viral nucleic acid to a new host/ uninfected cell. There are three basic capsid structures Icosahedral Helical complex Icosahedral Capsid structure Twelve vertices (corners) 20 triangular sides (faces) Symmetry (5:3:2) Composed of capsomes (which are the building blocks of the capsid). There are two types of capsomer: o Penton capsomers (Present on each vertice; therefore 12 are present in the capsid) o Hexon capsomers (variable number present) Example: Adenovirus (Type 1 ds DNA virus) Non enveloped icosahedral virus particle Capsid is built of 252 capsomers 12 penton capsomers situated at the apices (or vertice) which have a penton fibre attached to the penton capsomes 240 hexon capsomers filling the rest of the structure Helical capsids Structural unit is a single capsid protein arranged as a helix Capsid proteins forms a spiral covering the helical genome All animal viruses with helical symmetry are enveloped Present on a few viruses with an icosahedral capsid Example Paramyxovirus (Type V ve ss RNA virus) Helical nucleocapsid containing the ss RNA genome Enveloped; Roughly spherical Can be much larger and more pleomorphic than icosahedral viruses Complex capsids Only mammalian virus with a complex capsid structure is the Pox virus (Type 1 ds DNA virus) Oval shape 200 -400 nm long Complex, large virus- The capsid has neither helical or an icosahedral structure Virus Envelope Virus envelope is composed of a lipid bilayer (which is derived from the host) embedded with viral proteins/glycoproteins which contain receptors that enable attachment to permissive cells. Also contain antigenic determinants (parts of the virus that are recognised by antibody) Envelope is acquired by budding - either at the o plasma membrane or o membranes of subcellular organelles such as the ER, Golgi or nucleus. Biological Properties of Enveloped viruses Remain infectious in the environment for a shorter period of time (rarely beyond a few hrs) Cause diseases more frequently associated with seasons (cold temperatures favour their survival in the environment) Transferred by direct contact or aerosol rather than fomites More rapidly eliminated from infected premises than non-enveloped viruses Enveloped viruses are released by budding allowing long term release of virus from infected cell without the death of the cell Biological properties of unenveloped viruses Environmentally stable: easily spread by fomites Can survive adverse conditions in the gut Released by cell lysis Virus Structural Proteins Capsid/ nucleoprotein o Functions to protect the nucleic acid genome and deliver it to the cell where it can replicate o Minimum requirements for a virus is nucleic acid surrounded by a capsid Envelope glycoproteins o Embedded in the virus envelope (host-derived lipid membrane) Virus Matrix protein o Some virus have a matrix protein that connects the virus envelope with the virus capsid (e.g Orthomyxoviruses) Viral enzymes o Can sometimes be structural components of the virus o Some viruses carry their own enzymes as they are needed before the virus can replicate o E.g. negative sense RNA viruses (influenza) Virus Non-structural proteins Not a structural component of the virus or virion Made in the infected cell Can be Enzymes (RNA polymerase; reverse transcriptase, proteases, helicases) Other proteins involved in regulation of virus replication (e.g. proteins that help the virus avoid the immune system) How virus structure impacts their biology RNA viruses are more variable (increased diversity) because of o Error prone nature of RNA dep RNA Polymerase o Segmented nature of their genome that allows reassortment to occur Presence or absence of a virus envelope determines the virus stability