Viruses, Viroids and Prions Lecture Notes PDF

Viruses, Viroids and Prions  Viruses Viruses are inert particles, incapable of metabolism & replication & are obligate intracellular parasites. They are non-living & are called infectious agents & not organisms. Viruses are divided broadly into two groups based on t...

Viruses, Viroids and Prions  Viruses Viruses are inert particles, incapable of metabolism & replication & are obligate intracellular parasites. They are non-living & are called infectious agents & not organisms. Viruses are divided broadly into two groups based on the cells they infect. Some viruses infect prokaryotic cells, and other viruses infect eukaryotic cells.  Viruses The viruses that infect bacteria are known as ‘bacteriophages’ or simply ‘phages’. Bacteriophages serve as a model to  understand the molecular biology  virus-host relationship  vehicle for horizontal gene transfer in bacteria. Bacteriophages can kill bacteria & thus are important  In limiting bacterial populations in nature.  To control bacterial and pathogen growth in foods.  As alternative to antibiotics in treating bacterial infections.  Viruses and their characteristics Most viruses are of small size & are about 100- 1000-fold smaller than the cell they infect. The smallest viruses are about 10nm in diameter. The largest Relative sizes of viruses viruses are about 800nm, Viruses are too small to be seen by the size of the light microscope & can be visualized smallest only with an electron microscope. bacterial cells.  Structure of viruses Viruses contain DNA or RNA (never contain both) surrounded by a protective protein coat called capsid (made up of capsomeres). If no additional covering other than capsid, virus is called naked or non-enveloped virus. Nearly all phages are naked.  Structure of viruses Many viruses have an envelope/lipid membrane that surrounds the capsid & are called enveloped viruses. Some viruses have a matrix protein inside the lipid layer. The envelope is usually acquired from the cytoplasmic membrane of the infected cell during viral release & thus is a lipid bilayer containing various proteins. Proteins which bind virus to the cells & project out from envelope /capsid are called attachment proteins or spikes.  Structure of viruses Virion can have one of the three different shapes. - The most common is ‘Icosahedral’ symmetry in which protein subunits are arranged in groups of equilateral triangles (20) similar to a soccer ball & appear spherical under electron microscope. - Helical or rod shape- less common shape. – Complex: more intricate and irregular structures e.g., phages.  Classification of animal viruses Classified into various groups based on 1. Genome structure: DNA or RNA, single stranded or double stranded, segmented or a single molecule. 2. Virus particle structure- isometric (icosahedral), helical (rod-shaped) or pleomorphic (irregular in shape) 3. Presence or absence of a viral envelope: naked or enveloped viruses.  Classification of animal viruses Some RNA viruses have ≥ one RNA molecule & are called segmented viruses e.g. – Influenza virus (8 RNA segments). Animal viruses are divided into several families, whose names end in –viridae and are italicized e.g., coronaviridae. – 14 families of RNA-containing viruses infect vertebrates. – 7 families of DNA-containing viruses infect vertebrates. (Check table 13.1 for details)  Classification of viruses Each family contain many genera whose names end with –virus (single word) such as Enterovirus. In contrast to bacterial nomenclature, viruses are commonly referred by their species name. Species name is usually the name of the disease they cause, and the names are not italicized e.g., Poliovirus. (Arboviruses)  Animal virus replication Understanding virus infection cycle is medically important as virus replication mostly depends upon virally coded enzymes which are potential target for antiviral drugs. A generalized infection cycle of animal viruses can be viewed as a five-step process.  Animal virus replication 1. Attachment The process of attachment (adsorption) is basically same in all virus-cell interactions. Virus attachment proteins/spikes bind to host cell receptors (glycoproteins) present on the cell membrane. Usually, ≥ one receptor is required for effective virus attachment e.g., HIV binds to 2 receptors for entering cell. As a virion must bind to specific receptors, a particular virus infects only a single or a limited number of cell types & most viruses can infect only a single species.  Animal virus replication 2. Entry and Uncoating The mechanism depends on whether the virion is enveloped or naked but, in all cases, entire virion is taken into the cell. Entry of enveloped viruses: Two mechanisms  Membrane fusion  Endocytosis e.g. HIV. Naked viruses enter only by endocytosis. Uncoating takes place before replication.  Animal virus replication 3. Synthesis of viral proteins and replication of the genome Production of viral particles needs 2 distinct but interrelated events. -Expression of viral genes to produce structural and catalytic proteins (enzymes) required for replication. -Synthesis of multiple copies of the viral genome. Three replication strategies. -Replication of DNA viruses Replication of RNA viruses Replication of reverse transcribing viruses  Animal virus replication 4. Assembly (Maturation) The protein capsid must be formed and then the genome and any necessary enzymes are packaged within it. Assembly process takes place in the nucleus or cytoplasm or near cell membrane, depending upon the virus. 5. Release Most enveloped viruses are released by budding, a process whereby they acquire the envelope from plasma membrane. But some may get envelop from Golgi apparatus or rough endoplasmic reticulum. Budding may not destroy the host cells.  Animal virus replication 5. Release (Continued) Naked viruses are released when host cell dies. Many viruses trigger a normal cellular process called ‘apoptosis’ or ‘program cell death’, prior the release of viral particles. The immune response directed towards eliminating the virus can also lead to the same process. Viruses released from the dead cells may invade any healthy cells in the vicinity. The infectious virion must leave one animal host to be transmitted to another host. Viral particles may be shed in feces, urine, genital secretions, blood, or mucus and saliva released from respiratory tract during coughing and sneezing.  Categories of Animal Virus Infections Viruses and animal hosts relationships can be divided into two major categories ‘acute & persistent infections’ based on the disease & the state of the virion in the host. Acute infections: – are characterized by the sudden onset of symptoms of a relatively short duration. – Results in productive infection & infected cell die with or without the release of virions. – Disease symptoms result because of localized or widespread tissue damage following cell death as well as damage caused by the immune response itself. – Host immune system may gradually eliminate the virus over a period of days to months and develop long-lasting immunity. Examples of acute infections: influenza, mumps, measles, and poliomyelitis.  Persistent infections Persistent infections, can continue for years, or even the life of the host with or without symptoms. Persistent infections are further divided into 2 categories 1. Chronic infections 2. Latent infections 1. Chronic infections – Characterized by the continuous production of low level of viral particles with or without symptoms e.g., hepatitis B. – Consequently, a person can transmit the virus to others even in the absence of symptoms. – Some people infected with hepatitis B become carriers of the virus, able to pass it to others through blood and body fluids.  Persistent infections 2. Latent infections Viral genome remains silent within the host cell yet can reactivate to direct a productive infection. Silent viral genome is called ‘provirus’ & it can integrate in host genome (e.g., HIV) or exist as independent of host genome. Provirus can cause disease even after a long period without symptoms e.g., Herpes simplex type I virus (HSV-1). HSV-1 causes an acute infection in mucosal epithelium leading to typical symptoms of cold sore. Then the virus can spread to sensory nerve cells where it remains latent. Later, latent virus can reactivate & cause another episode of cold sore. Infection cycle of HSV-1 What reactivate the virus is not clear but may involve certain physiological or immunological changes.  Viral infections We often categorize viral infections as acute or persistent, they do not always fall neatly into a single category. Example: HIV infection has features of both acute and persistent infections.  Viruses and human tumors Tumor: is an abnormal growth of a tissue. Two types: Benign tumor (do not spread) and malignant /cancerous tumor (has potential to metastasize). Most human tumors are not caused by viruses. DNA viruses are the main cause of virus-induced tumors in humans except retroviruses (RNA viruses).  Cultivating Animal viruses As viruses can grow only inside living cells, various types of cells are used to study virus growth. Some viruses can be – cultivated in living animals only. – grown in embryonated chicken eggs e.g., influenza viruses are grown in chicken eggs to prepare vaccines. – grown in human or animal cells (not all viruses). The host cells are cultivated by a technique called ‘cell or tissue culture’. Today primary cultures, established cell lines & tumor cell lines are used for growing viruses.  Effects of viral replication on cell cultures Many viruses can be detected by their effects on cells in cell cultures. The virus grown with susceptible cells often causes distinct morphological alterations in infected cells referred as cytopathic effect. The infected host cells may change the shape, detach from the surface or lyse. Infected cell may fuse into a giant Cytopathic effect of multinuclear cell (syncytium), a virus infection mechanism of spread e.g., HIV & measles. Inclusion body type varies Certain viruses cause an infected cell depending upon to form a distinct region called an the virus and can inclusion body (site of viral be used for virus replication). identification.  Quantitation of viruses 1. Plaque assay: – Most precise & commonly used method. – Sample containing virus is added to monolayer of actively metabolizing cells. – Infection and lysis – Each plaque represents one of infected cells virion initially infecting one cell leads to a clear & so number of virions in original zone or plaque samples can be determined. surrounded by the uninfected cells. – Plaques are only formed by infective viruses & can be used with any viruses that lyse host cells.  Quantitation of viruses cont’d 2. Virions counting with electron microscope This method is used if pure preparation of viruses is obtained. May distinguish between infective & non-infective virions. Calicivirus Virus shape & size may provide clues for the identify of virus.  Quantitation of viruses cont’d 3. Quantal assays Usually provide an approximate virus concentration. In this assay, several dilutions of the virus are administered to a number of animals, cells or chick embryos, depending host specificity of the virus. The titer of the virus, or the end point is the dilution at which 50% of the inoculated hosts are infected or killed. Titer is reported as either ID50 (infective dose), or the LD50 (lethal dose).  Quantitation of viruses cont’d 4. Hemagglutination Some animal viruses clump or agglutinate RBCs as they interact with the surfaces of these cells. This phenomenon is called hemagglutination. Example: Orthomyxoviruses. Influenza virus is a member of this group Measured by using various dilutions of the virus with a standard amount of RBC. The highest dilution showing maximum agglutination is the titer of the virus.  Prions Prions contain protein only and no nucleic acid which is reflected in the name (proteinacious infectious agents). Cause number of slow, fatal human and animal diseases and symptoms appear many years after the infection. In prion diseases, prion protein accumulate in neural tissue. For unknown reasons brain function deteriorates as neurons die & brain tissue develops spongelike holes. Because of characteristic spongelike appearance of the brain tissue, the general term transmissible spongiform encephalopathies (TSEs) is used for all these diseases. Prion Diseases  Prions A protein similar in its amino acid composition to prion protein is synthesized in normal, uninfected cells especially in neurons in the brain tissue. This ‘normal prion protein’ is designated as PrPC (Prion protein cellular) The tertiary structure of ‘disease causing prion protein’ called PrPsc (Prion protein scrapie) is different from PrPC. PrPsc is resistant to protease (Proteinase K) digestion whereas PrPC is sensitive to protease digestion. This property is used for the diagnosis of prion diseases.  Prions cont’d Prions contain no nucleic acids & thus are not inactivated by UV light or nucleases. Prions are unusually resistant to heat and chemical treatments that are commonly used to inactivate infectious agents. The prion protein replicates by converting the normal host protein PrPC into disease causing prion protein PrPsc, thereby creating more prion protein molecules. The prion protein is infectious as it catalyzes the conversion of normal protein into prion protein.  Prions cont’d In most cases, the prion protein is only transmitted to members of the same species, because of differences in prion protein amino acid sequences among species. But the barrier to prion transmission between species also vary on the strain of prion. Prions that caused ‘mad cow disease’ caused a human disease very similar to Creutzefeldt-Jacob disease (CJD). This disease killed more than 170 people who ate beef/tissues of infected animals. Thus, it is a disease of public health and economic importance. Scrapie of sheep & chronic wasting disease (CWD) of deer & elk have not been shown to be transmitted to humans. CWD spread among deer population in Canada and USA though animal-to-animal (nose-to-nose) contact.  Next lecture Chapter 5 (Control of Microbial Growth)