Virus PDF

VIRUS The general properties and structure of viruses Virus reproduction / replication Cultivation and quantification of viruses Principles of virus taxonomy Viral diversity and other acellular infection agents Vaccine and antiviral agent Assoc. Prof. Dr. Nur Ain Izzati Mohd Zainudin...

VIRUS The general properties and structure of viruses Virus reproduction / replication Cultivation and quantification of viruses Principles of virus taxonomy Viral diversity and other acellular infection agents Vaccine and antiviral agent Assoc. Prof. Dr. Nur Ain Izzati Mohd Zainudin Universiti Putra Malaysia Learning outcomes By the end of this lecture, students will be able to: 1. To explain about virus taxonomy and diversity of virus 2. To explain about the structure of virus, replication and transfer of virus 3. To list the characteristics of virus 4. To explain about acellular infection agent 5. To explain about quantification of virus and virus purification Assessment of current and prior knowledge Please, complete in 10 minutes. 1. Viruses are noncellular, why? 2. How to avoid from viral infection? OUTLINE: VIRUS 1. The general properties and structure of viruses 2. Virus reproduction / replication 3. Cultivation and quantification of viruses 4. Principles of virus taxonomy 5. Viral diversity and other acellular infection agents 6. Antiviral agents Introduction Viruses are quite different from prokaryotic and eukaryotic microorganisms. Virologists – who studied on virus Virology – the study of viruses Viruses are noncellular - do not have a cellular structure. Lack most of the components of cells, such as organelles, ribosomes, and the plasma membrane. Early development of virology Europeans were first protected from a viral disease when Edward Jenner developed a smallpox vaccine in 1798. Viruses were first discovered after the development of the Chamberland-Pasteur filter that could remove all bacteria visible in the microscope from any liquid sample to show that viruses were different from bacteria. In the late 1930s Stanley, Bawden and Pirie crystallized the tobacco mosaic virus and demonstrated that it was composed only of protein and nucleic acid. 1. The general properties and structure of viruses 1.The general properties and structure of viruses Viruses are simple, acellular entities. They can reproduce only within living cells because they are obligate intracellular parasites. Viruses can exist in two phases: extracellular and intracellular. Virions, the extracellular phase, possess few if any enzymes and cannot reproduce independent of living cells. In intracellular phase, virus exist primarily as replicating nucleic acid that induce host metabolism to synthesize virion component. The general properties Viruses are simple, acellular entities. They can reproduce only within living cells because they are obligate intracellular parasites. Viruses can exist in two phases: extracellular and intracellular. Virions, the extracellular phase, possess few if any enzymes and cannot reproduce independent of living cells. In intracellular phase, virus exist primarily as replicating nucleic acid that induce host metabolism to synthesize virion component. The structure of viruses All virions have a nucleocapsid composed of a nucleic acid, usually consist of one or more molecules DNA or RNA (but not both), enclosed in a coat of protein of virions. Protein capsid made of one or more types of protein subunits called protomers. Viral capsid can be: ❖ Helical ❖ Icosahedral ❖ Complex The structure of viruses Those virions having an envelope are called enveloped viruses; whereas those lacking an envelope are called naked viruses. Morphology of viruses The size and morphology of selected virus The structure of viruses Helical capsids: ❖ The capsids are shaped like hollow tubes with protein walls and may be either rigid or quite flexible. ❖ The self-assembly of protomers in a helical or spiral arrangement produce a long, rigid tube, 15 to 18 nm in diameter by 300 nm long. ❖ The capsid enclosed an RNA genome, the nucleic acid is coiled in a spiral on the inside of the cylinder. ❖ The tabacco mosaic provides a well-studied example of helical capsid structure. The structure of viruses Adenovirus Canine parvovirus model The structure of viruses Complex viruses: ❖ e.g. poxviruses and large phage. ❖ Viruses with capsids of complex symmetry. ❖ They have complicated morphology not characterized by icosahedral and helical symmetry. ❖ Large phages often have binal symmetry; their heads are icosahedral and their tails, helical. The structure of viruses Icosahedral capsids: ❖ The icosahedron is a regular polyhedron with 20 equilateral triangular faces and 12 vertices. ❖ The capsids are usually constructed from ring or knob-shaped units called capsomers, each usually made of five or six protomers. ❖ The two types of capsomers: a) pentamers (pentons) at the verticals b) hexamers (hexons) on the edges and faces of the icosahedron The structure of viruses ❖ The poxviruses are the largest of the animal viruses (400 x 240 x 200 nm in size) and can even be seen with a phase-contrast microscope or in stained preparations. ❖ The double stranded DNA is associated with protein and contained in the nucleoid, a central structure shaped like a biconcave disk and surrounded by a membrane. The structure of viruses ❖ e.g. poxvirus is vaccinia virus The structure of viruses ❖ The ecosahedral head is elongated by one or two row of hexamers in the middle and contains the DNA genome. ❖ The tail is imposed of a collar joining it to the head, a central hollow tube, a sheath surrounding the tube, and a complex baseplate. ❖ They are binal symmetry because they have a head that resembles an icosahedron and a tail that is helical. The structure of viruses Viral envelopes and enzyme ❖ Many viruses are bounded by an outer membranous layer called envelope, that surrounding their nucleocapsid. ❖The envelope lipids usually come from the host cell nuclear or plasma membrane. ❖ Many envelope proteins are coded for by virus genes and may even project from the envelop surface as spikes, which are also called peplomers. ❖Spikes are involved in virus attachment to the host cell surface. Enveloped Viruses Enveloped Viruses ❖ The envelop is a flexible, membranous structure. ❖ Envelop viruses frequently have a somewhat variable shape and are called pleomorphic. ❖ Some the envelopes of viruses like bullet-shaped rabies virus are firmly attached to the underlying nucleocapsid and endow the virion with a constant, characteristics shape. ❖ In some viruses the envelope is disrupted by solvent like ether; the virus is then said to be ‘ether sensitive’ The structure of viruses ❖ In influenza virus, the enzymes are associated with the envelope or capsid (e.g. influenza neuraminidase), but most viral enzymes are located within the capsid. ❖ Many of these are involved in nucleic acid replication. ❖ Such enzymes are called RNA-dependent RNA polymerase. ❖ Although viruses lack true metabolism, some contain a few enzymes necessary for their reproduction / life cycles.  TURN AND TALK In pairs, you are given 10 minutes to draw, label and elaborate naked and envelope viruses Viral genomes ❖ Viral nucleic acid can be either: - single-stranded DNA - double stranded DNA - single-stranded RNA - double stranded RNA ❖ All 4 types are found in animal viruses. ❖ Most plant viruses have single-stranded DNA. Viral genomes ❖ RNA viruses usually have ssRNA that may be either plus (+ve) or minus (-ve) when compared with mRNA (+ve). ❖ Many RNA genome are segmented – that is genome consists of more than one RNA strand or segments. ❖ Each segment codes for one protein. Usually all segments are enclosed in the same capsid even though some virus genomes may be composed as many as 10 to 12 segments. COVID-19 The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. - an enveloped and spherical particle - ~120 nm in diameter - a positive single-stranded RNA genome. - subfamily Corona-virinae, family Coronavirdiae, and order Nidovirales. - The RNA genome of SARS-CoV-2 contains a 50 methyl-guanosine cap, poly (A)-tail, and 29,903 nucleotides. - classified as a beta-coronavirus (bCoV) - the seventh member of the coronavirusfamily to infect humans 2. Virus reproduction / replication 2. Virus reproduction / replication Virus reproduction can be divided into five steps: 1) Attachment (adsorption) of the virion to a susceptible host cell, 2) Penetration (injection) of the virion or the viral nucleic acid into the host, 3) Synthesis of viral nucleic acid and proteins – viral genes are transcribed and translated, control the host cell’s machinery – replicated and protein synthesized 4) Self-assembly of capsomer (and membrane components in enveloped viruses) and packaging of nucleic acid into new virions and; 5) Release of mature virions from the cell host. Virus reproduction Step 1 Step 2 Step 3 Step 5 Step 4 https://youtu.be/QHHrph7zDLw?si=WfgTRHi3Aa5x5mZ_ 3. The Cultivation of viruses 3. The cultivation of viruses Because viruses are unable to reproduce independent of living cells, viruses cannot be cultured in the same way as prokaryotic and eukaryotic microorganisms. Viruses are cultivated using tissue cultures, embryonated eggs, bacterial cultures and other living hosts. Sites of animal viral infection may be characterized by cytopathic effects such as pock and plaques. Phages produce plaques in bacterial lawns. Plant viruses can cause localized necrotic lesions in plant tissue. 3. Cultivation of viruses: 1) Fertilized chicken eggs were incubated about 6-8 days after laying. 2) The shell surface disinfected with iodine and penetrated with the small sterile drill. 3) Injected virus in the allantoic cavity. 4) Drill hole is sealed with gelatin. 5) The inoculated egg incubated. The Quantification of viruses Counting using electron microscope - viruses particle can be counted directly with the TEM or indirectly by the hemagglutination assay. Quantification of viruses: Plaque assay – A zone of lysis that infected may occur a clear area, this clearing is called a plaque, and it is assumed that each plaque has originated from replication events that began with one virion. By counting the plaque - forming units, can calculate the number of virus infectious units present in the original sample  Whole animal methods ❖ Quantification can be done only by in titration in infected animals. ❖ The general procedure is to carry out a serial dilution of the unknown sample and inject samples of each dilution into several sensitive animals. ❖ Virus numbers estimated in terms of lethal dose (LD50 - half of the animal injected died) or infectious dose (ID50). Virus purification The plaque procedure also permits the isolation of pure virus stains. Virus can be purified by techniques such as differential and gradient centrifugation, precipitation and denaturation or digestion of contaminants. 4. Principles of virus taxonomy 4. Principles of virus taxonomy International committee for taxonomy of viruses (ICTV) developed a uniform classification system. ICTV described almost 2000 virus species and place them in 3 orders, 73 families, 9 subfamilies and 287 genera. Currently, viruses are classified with a taxonomic system placing primary emphasis on the type and strandedness of viral nucleic acids, and on the presence or absence of an envelope. Alternative classification scheme devised by David Baltimore. The Baltimore system of virus classification is used by many virologists to organized virus based on their genome type and the mechanisms they use to synthesize mRNA and replicate their genome. Principles of virus taxonomy 5. Viral diversity and other acellular infection agents Bacterial viruses Bacteriophages quite diverse. Most of bacteriophages contain dsDNA; some ssRNA, dsRNA and ssDNA. Many bacterial virus structurally complex. A few bacterial viruses are lipid envelopes, but some naked. The tails of bacteriophages T2, T4, and Mu are contractile and are involved in nucleic acid penetration of the host. In contrast, the tail of phage Lambda is flexible. Four families contain archaeal bacterial viruses having unusual capsid morphologies. Animal and human viruses Eukaryotic viruses are classified according to many properties; based primarily on genome structure, replication strategy, morphology and genetic relatedness; the most important are their nucleic acids and replicative strategies. Fig 18.2: The taxonomy of DNA animal viruses Fig 18.3: The taxonomy of RNA animal viruses Their nucleic acid can be ss or ds, circular or linear. The reproduction of animal viruses is very similar in phages; that divided into: adsorption, penetration, replication of viral nucleic acids and synthesis of viral proteins, assembly of viral capsids and release of mature viruses.  Viruses and cancer ❖ Cancer is characterized by the formation of a malignant tumor that metastasizes or invades other tissues and can spread through the body. ❖ Carcinogenesis is a complex, multi steps process involving many factors. ❖ Viruses cause cancer in several ways, e.g they may bring a cancer-causing agent, or oncogene into a cell, or the virion may insert a transcription regulatory element next to a cellular proto-oncogene and stimulate the gene to greater activity. ❖ Viral protein may inactivate tumor-suppressor proteins, thereby promoting hyperproliferation and mutation. Examples of human viruses: ❖ The Epstein-Barr virus (EBV) – herpesvirus that cause Burkitt’s lymphoma and nasopharyngeal carcinoma Examples of human viruses: ❖ Hepatitis B virus – associated with liver cancer (hepatocellular carcinoma) and can be integrated into the human genome. Examples of human viruses: ❖ Hepatitis C virus – causes cirrhosis of the liver Examples of human viruses: ❖ Human herpesvirus and HIV associated with the development of Karosi’s sarcoma Examples of human viruses: ❖ Human papillomaviruses – linked to cervical cancer HPV, or human papillomavirus, is the most common STI in the U.S.Md Saiful Islam Khan / Getty Images/iStockphoto Examples of human viruses: ❖ Two retroviruses: The human T-cell lymphotropic virus 1 (HTLV-1) and HTLV-2 – associated with adult T-cell leukemia and hairly-cell leukemia, respectively. Plant viruses Entry of plant viruses into their host is usually mediated by mechanical damage to the plant. These creates openings in the plant cell walls through which the virus can enter. Plant-feeding animals, especially insects, or often the cause of this damage. Plant viruses Most of plant viruses have an RNA genome and may be either helical or icosahedral. Depending on the virus the RNA genome may be replicated by either a host RNA-dependent RNA polymerase or a virus-specific RNA replicase. The TMV nucleocapsid forms spontaneously by self-assembly when disks of coat protein promoters complex with the RNA.  Viruses of fungi Mycoviruses from higher isometric capsids and dsRNA, whereas the viruses of the lower fungi may have either dsRNA and dsDNA genomes.  Viruses of protists Only a few viruses of protists have been isolated and studied. Some have extremely large dsDNA genomes that include genes not usually found in viral genomes. Thin section electron micrograph of an uninfected Cafeteria roenbergensis cell. B) C. roenbergensis cell infected with CroV. Images by U. Mersdorf.  Insects viruses Member of several virus families infect insects and many of these viruses produce inclusion bodies that aid in their transmission. e.g. Granulosis viruses (Baculoviruses – rod shape, enveloped virus of helical symmetry and with dsDNA) form granular protein inclusions, usually in the cytoplasm Ultrastructural analysis of Diatraea saccharalis granulovirus (DisaGV). Transmission electron micrograph reveals granular occlusion bodies containing singly embedded rod-shaped nucleocapsid (scale bars = 0.5 μ m) Insects viruses Faviviridae and Togaviridae, whose members cause yellow fever, west Nile disease, and several types of viral encephalitis. Other viruses use insects as primary hosts; Baculoviridae, Reoviridae and Polydnaviridae uses and other viruses are finding uses as biological control agents for insects pests. Viroid and virusoids Infectious agents simpler than viruses exists. For example, several plants diseases are caused by short strands of infectious RNA called viriods. Virusoids are infectious RNAs that encode one or more gene products. They require a helper virus for replication. Prions Prions are small proteinaceous agents associated with at least six degenerative nervous system disorders: scapie, bovine spongiform encephalopathy, kuru, fatal familial insomnia, the Gerstman-Strässler-Scheinker syndrome, and Creutzfeldt-Jakob disease. The precise nature of prions is not yet clear. Most evidence supports the hypothesis that prion proteins exist in two forms: the infectious, abnormally folded form and a normal cellular form. The infection between the abnormal form and the cellular form converts the cellular form into the abnormal form. 6. Vaccines and antiviral agents Vaccines A vaccine is a biological preparation that improves immunity to a particular disease. A vaccine typically contains an agent that resembles a disease-causing microorganism, and is often made from weakened or killed forms of the microbe, its toxins or one of its surface proteins. Vaccines are dead or inactivated organisms or purified products derived from them. There are several types of vaccines in use. 1. Inactivated Some vaccines contain killed, but previously virulent, - e.g. Influenza vaccine, cholera vaccine, bubonic plague vaccine, polio vaccine, hepatitis A vaccine, and rabies vaccine. 2. Attenuated Some vaccines contain live, attenuated microorganisms. - e.g. Yellow fever, measles, rubella, and mumps. 3. Subunit Protein subunit- rather than introducing an inactivated or attenuated micro- organism to an immune system (which would constitute a "whole-agent" vaccine), a fragment of it can create an immune response. - e.g subunit vaccine against Hepatitis B 4. DNA Vaccine H1N1 flu nasal spray DNA vaccine concept has been tested and applied against various pathogens as an example of attenuated vaccine and tumor antigens 6. Vaccines and antiviral agents Antivirals are medications that help your body fight off certain viruses that can cause disease. Antiviral drugs are also preventive. Before cell entry - to interfere with the ability of a virus to infiltrate a target cell - A number of "entry- inhibiting" or "entry- blocking" drugs are being developed to fight Release phase HIV - Target the release of completed viruses from the host cell - Two drugs named zanamivir During viral synthesis (Relenza) and oseltamivir (Tamiflu) - to target the processes that synthesize virus components after a virus invades a cell. - Invirase®, Fortovase®. How a virus works: https://www.youtube.com/watch?v=SBfv-0g3EvE Mader, S. S., & Windelspecht, M. (2019). Biology (13th ed.). McGraw-Hill Education. Urry, L. A. Cain, M. L. Wasserman, S. A. Minorsky, P. V. Reece, J. B.(2020). Campbell Biology (11th ed.). Pearson Benjamin Cummings. Madigan, M. T. Bender, K. S. Buckley, D. H. Sattley, W. M. & Stahl, D. A. (2020). Brock Biology of Microorganisms. (16th ed.). Pearson.