Medical Virology PDF

Medical Virology Mohammed A Mamash I - OVERVIEW A virus is an infectious agent that is minimally :constructed of two components a genome consisting of either ribonucleic )1 acid (RNA) or deoxyribonucleic acid (DNA), but not both a protein-containing structure (capsid) )2 designed to protec...

Medical Virology Mohammed A Mamash I - OVERVIEW A virus is an infectious agent that is minimally :constructed of two components a genome consisting of either ribonucleic )1 acid (RNA) or deoxyribonucleic acid (DNA), but not both a protein-containing structure (capsid) )2 designed to protect the genome Man viruses have additional structural features, for example, an envelope composed of a protein-containing lipid bilayer, whose presence or absence further.distinguishes one virus group from another Viruses are obligate intracellular parasites that do not have a cellular structure. Rather, a virus consists of molecule(s) of DNA (DNA virus) or RNA (RNA virus), but not both,.surrounded by a protein coat A virus may also have an envelope derived from the plasma membrane of the host cell from which the virus is released. Viruses contain the genetic information necessary for directing their own replication but require the host’s cellular structures and enzymatic machinery to.complete the process of their own reproduction The fate of the host cell following viral infection ranges from rapid lysis and release of many progeny virions to gradual,.prolonged release of viral particles A complete virus particle combining these structural elements is called a virion. In functional terms, a virion can be envisioned as a delivery system that surrounds a nucleic acid payload. The delivery system is designed to protect the genome and enable the virus to bind to host cells. The payload is the viral genome and may also include enzymes required for the initial steps in viral replication—a process that is obligately intracellular. The pathogenicity of a virus depends on a great variety of structural and functional characteristics. Therefore, even within a closely related group of viruses, different species may produce significantly distinct clinical pathologies.  II - CHARACTERISTICS USED TO DEFINE VIRUS FAMILIES, GENERA, AND SPECIES Viruses are divided into related groups, or families, and, sometimes into subfamilies based on: 1) type and structure of the viral nucleic acid. 2) the strategy used in its replication. 3) type of symmetry of the virus capsid (helical versus icosahedral. 4) presence or absence of a lipid envelope. Within a virus family, differences in additional specific properties, such as host range, serologic reactions, amino acid sequences of viral proteins, degree of nucleic acid homology, among others, form the basis for division into genera (singular, genus) and species. Species of the same virus isolated from different geographic locations may differ from each other in nucleotide sequence. In this case, they are referred to as strains of the same species. A. Genome The type of nucleic acid found in the virus particle is perhaps the most fundamental and straightforward of viral properties. It may be RNA or DNA, either of which may be single stranded (ss) or double stranded (ds). The most common forms of viral genomes found in nature are ssRNA and dsDNA. However, both dsRNA and ssDNA genomes are found in viruses of medical significance. Single-stranded viral RNA genomes are further subdivided into those of “positive polarity” (that is, of messenger RNA sense, which can, therefore, be used as a template for protein synthesis) and those of “negative polarity” or are antisense (that is, complementary to messenger RNA sense, which cannot, therefore, be used directly as a template for protein synthesis). Viruses containing these two types of RNA genomes are commonly referred to as positive-strand and negative- strand RNA viruses, respectively. B. Capsid symmetry The protein shell enclosing the genome is, for most virus families, found in either of two geometric configurations helical (rod shaped or coiled) or icosahedral (spherical or.symmetric) The capsid is constructed of multiple copies of a single polypeptide type (found in helical capsids) or a small number of different polypeptides (found in icosahedral capsids), requiring only a limited amount of genetic information to code for these structural components Helical symmetry: Capsids with.1 helical symmetry, such as the paramyxoviridae, consist of repeated units of a single polypeptide species that—in association with the viral nucleic acid—self-assemble into a.helical cylinder Each polypeptide unit (protomer) is hydrogen-bonded to neighboring protomers. The complex of protomers and nucleic acid is called the nucleocapsid. Because the nucleic acid of a virus is surrounded by the capsid, it is protected from environmental.damage 2. Icosahedral symmetry: Capsids with icosahedral symmetry are more complex than those with helical symmetry, in that they consist of several different polypeptides grouped into structural subassemblies called capsomers. These, in turn, are hydrogen-bonded to each other to form an icosahedron. The nucleic acid genome is located within the empty space created by the rigid, icosahedral structure. C. Envelope An important structural feature used in defining a viral family is the presence or absence of a lipid-containing membrane surrounding the nucleocapsid. This membrane is referred to as the envelope. A virus that is not enveloped is referred to as a naked virus. In enveloped viruses, the nucleocapsid is flexible and coiled within the envelope, resulting in most such viruses appearing to be roughly spherical. The envelope is derived from host cell membranes. However, the cellular membrane proteins are replaced by virus-specific proteins, conferring virus- specific antigenicity upon the particle. Among viruses of medical importance, there are both naked and enveloped icosahedral viruses, but all the helical viruses of animals are enveloped and contain RNA. III. VIRAL REPLICATION: THE ONE-STEP GROWTH CURVE The one-step growth curve is a representation of the overall change, with time, in the amount of infectious virus in a single cell that has been infected by a single virus particle. In practice, this is determined by following events in a large population of infected cells in which the infection is proceeding as nearly synchronously as can be achieved by manipulating the experimental conditions. Whereas the time scale and yield of progeny virus vary greatly among virus families, the basic features of the infectious cycle are similar for all viruses. The one-step growth curve begins with the eclipse period, which is followed by a period of exponential growth A. Eclipse period Following initial attachment of a virus to the host cell, the ability of that virus to infect other cells disappears. This is the eclipse period, and it represents the time elapsed from initial entry and disassembly of the parental virus to the assembly of the first progeny virion. During this period, active synthesis of virus components is occurring. The eclipse period for most human viruses falls within a range of 1 to 20 hours. B. Exponential growth The number of progeny virus produced within the infected cell increases exponentially for a period of time, then reaches a plateau, after which no additional increase in virus yield occurs. The maximum yield per cell is characteristic for each virus-cell system and reflects the balance between the rate at which virus components continue to be synthesized and assembled into virions, and the rate at which the cell loses the synthetic capacity and structural integrity needed to produce new virus particles. This may be from 8 to 72 hours or longer, with yields of 100 to 10,000 virions per cell. IV. STEPS IN THE REPLICATION CYCLES OF VIRUSES The individual steps in the virus replication cycle are presented below in sequence, beginning with virus attachment to the host cell and leading to penetration and uncoating of the viral genome. Gene expression and replication are followed by assembly and release of viral progeny. A. Adsorption The initial attachment of a virus particle to a host cell involves an interaction between specific molecular structures on the virion surface and receptor molecules in the host cell membrane that recognize these viral structures 1. Attachment sites on the viral surface: Some viruses have specialized attachment structures such as the glycoprotein spikes found in viral envelopes (for example, rhabdoviruses, whereas, for others, the unique folding of the capsid proteins forms the attachment sites (for example, picornaviruses. In both cases, multiple copies of these molecular attachment structures are distributed around the surface of the virion. [Note: In some cases, the mechanism by which antibodies neutralize viral infectivity is through antibody binding to the viral structures that are required for adsorption.] 2. Host cell receptor molecules: The receptor molecules on the host cell membrane are specific for each virus family. Not surprisingly, these receptors have been found to be molecular structures that usually carry out normal cell functions. For example, cellular membrane receptors for compounds such as growth factors may also inadvertently serve as receptors for a particular virus. Many of the compounds that serve as virus receptors are present only on specifically differentiated cells or are unique for one animal species. Therefore, the presence or absence of host cell receptors is one important determinant of tissue specificity within a susceptible host species and also for the susceptibility or resistance of a species to a given virus. Information about the three-dimensional structure of virus-binding sites is being used to design antiviral drugs that specifically interact with these sites, blocking viral adsorption. B. Penetration Penetration is the passage of the virion from the surface of the cell across the cell membrane and into the cytoplasm. There are two principal mechanisms by which viruses enter animal cells: receptormediated endocytosis and direct membrane fusion. 1. Receptor-mediated endocytosis: This is basically the same process by which the cell internalizes compounds, such as growth regulatory molecules and serum lipoproteins, except that the infecting virus particle is bound to the host cell surface receptor in place of the normal ligand. The cell membrane invaginates, enclosing the virion in an endocytotic vesicle (endosome). Release of the virion into the cytoplasm occurs by various routes, depending on the virus, but, in general, it is facilitated by one or more viral molecules. In the case of an enveloped virus, its membrane may fuse with the membrane of the endosome, resulting in the release of the nucleocapsid into the cytoplasm. Failure to exit the endosome before fusion with a lysosome generally results in degradation of the virion by lysosomal enzymes. Therefore, not all potentially infectious particles are successful in establishing infection. 2. Membrane fusion: Some enveloped viruses (for example, human immunodeficiency virus) enter a host cell by fusion of their envelope with the plasma membrane of the cell. One or more of the glycoproteins in the envelope of these viruses promotes the fusion. The end result of this process is that the nucleocapsid is free in the cytoplasm, whereas the viral membrane remains associated with the plasma membrane of the host cell. C. Uncoating “Uncoating” refers to the stepwise process of disassembly of the virion that enables the expression of the viral genes that carry out replication. For enveloped viruses, the penetration process itself is the first step in uncoating. In general, most steps of the uncoating process occur within the cell and depend on cellular enzymes. However, in some of the more complex viruses, newly synthesized viral proteins are required to complete the process. The loss of one or more structural components of the virion during uncoating predictably leads to a loss of the ability of that particle to infect other cells, which is the basis for the eclipse period of the growth curve. It is during this phase in the replication cycle that viral gene expression begins D. Mechanisms of DNA virus genome replication Each virus family differs in significant ways from all others in terms of the details of the macromolecular events comprising the replication cycle. The wide range of viral genome sizes gives rise to great differences in the number of proteins for which the virus can code. In general, the smaller the viral genome, the more the virus must depend on the host cell to provide the functions needed for vira replication. For example, some small DNA viruses, such as Polyomaviruses, produce only one or two replicationrelated gene products, which function to divert host cell processes to those of viral replication. Other larger DNA viruses, such as poxviruses, provide virtually all enzymatic and regulatory molecules needed for a complete replication cycle. Most DNAviruses assemble in the nucleus, whereas most RNA viruses develop solely in the cytoplasm. F. Assembly and release of progeny viruses Assembly of nucleocapsids generally takes place in the host cell compartment where the viral nucleic acid replication occurs (that is, in the cytoplasm for most RNA viruses and in the nucleus for most DNA viruses). For DNA viruses, this requires that capsid proteins be transported from their site of synthesis (cytoplasm) to the nucleus. The various capsid components begin to self- assemble, eventually associating with the nucleic acid to complete the nucleocapsid. 1. Naked viruses: In naked (unenveloped) viruses, the virion is complete at this point. Release of progeny is usually a passive event resulting from the disintegration of the dying cell and, therefore, may be at a relatively late time after infection. 2. Enveloped viruses: In enveloped viruses, virus-specific glycoproteins are synthesized and transported to the host cell membrane in the same manner as cellular membrane proteins. When inserted into the 1 membrane, they displace the cellular glycoproteins, resulting in patches on the cell surface that have viral antigenic specificity. The cytoplasmic domains of these proteins associate specifically with one or more additional viral proteins (matrix proteins) to which the nucleocapsids bind. Final maturation then involves envelopment of the nucleocapsid by a process of “budding”. A consequence of this mechanism of viral replication is that progeny virus are released continuously while replication is proceeding within the cell and ends when the cell loses its ability to maintain the integrity of the plasma membrane. A second consequence is that, with most enveloped viruses, all infectious progeny are extracellular. The exceptions are those viruses that acquire their envelopes by budding through internal cell membranes such as those of the endoplasmic reticulum or nucleus. Viruses containing lipid envelopes are sensitive to damage by harsh environments and, therefore, tend to be transmitted by the respiratory, parenteral, and sexual routes. Nonenveloped viruses are more stable to hostile environmental conditions and often transmitted by the fecal–oral route.  G. EFFECTS OF VIRAL INFECTION ON THE HOST CELL The response of a host cell to infection by a virus ranges from: 1) little or no detectable effect 2) alteration of the antigenic specificity of the cell surface due to presence of virus glycoproteins 3) latent infections that, in some cases, cause cell transformation 4) cell death due to expression of viral genes that shut off essential host cell functions 1. VIRAL INFECTIONS IN WHICH NO PROGENY VIRUS ARE PRODUCED: IN THIS CASE, THE INFECTION IS REFERRED TO AS ABORTIVE. AN ABORTIVE RESPONSE TO INFECTION IS COMMONLY CAUSED BY: 1) A NORMAL VIRUS INFECTING CELLS THAT ARE LACKING IN ENZYMES, PROMOTERS, TRANSCRIPTION FACTORS, OR OTHER COMPOUNDS REQUIRED FOR COMPLETE VIRAL REPLICATION, IN WHICH CASE THE CELLS ARE REFERRED TO AS NONPERMISSIVE; 2) INFECTION BY A DEFECTIVE VIRUS OF A CELL THAT NORMALLY SUPPORTS VIRAL REPLICATION (THAT IS, BY A VIRUS THAT ITSELF HAS GENETICALLY LOST THE ABILITY TO REPLICATE IN THAT CELL TYPE). 3) DEATH OF THE CELL AS A CONSEQUENCE OF THE INFECTION, BEFORE VIRAL REPLICATION HAS BEEN COMPLETED. 2. VIRAL INFECTIONS IN WHICH THE HOST CELL MAY BE ALTERED ANTIGENICALLY BUT IS NOT KILLED, ALTHOUGH PROGENY VIRUS ARE RELEASED: IN THIS CASE, THE HOST CELL IS PERMISSIVE, AND THE INFECTION IS PRODUCTIVE (PROGENY VIRUS ARE RELEASED FROM THE CELL), BUT VIRAL REPLICATION AND RELEASE NEITHER KILLS THE HOST CELL NOR INTERFERES WITH ITS ABILITY TO MULTIPLY AND CARRY OUT DIFFERENTIATED FUNCTIONS. THE INFECTION IS, THEREFORE, SAID TO BE PERSISTENT. THE ANTIGENIC SPECIFICITY OF THE CELL SURFACE MAY BE ALTERED AS A RESULT OF THE INSERTION OF VIRAL GLYCOPROTEINS. 3. Viral infections that result in a latent viral state in the host cell: Some viral infections result in the persistence of the viral genome inside a host cell with no production of progeny virus. Such latent viruses can be reactivated months or years in the future, leading to a productive infection. Some latently infected cells contain viral genomes that are stably integrated into a host cell chromosome. This can cause alterations in the host cell surface; cellular metabolic functions; and, significantly, cell growth and replication patterns. Such viruses may induce tumors in animals, in which case they are said to be tumor viruses, and the cells they infect are transformed. 4. Viral infections resulting in host cell death and production of progeny virus: Eliminating host cell competition for synthetic enzymes and precursor molecules increases the efficiency with which virus constituents can be synthesized. Therefore, the typical result of a productive (progeny-yielding) infection by a cytocidal virus is the shutoff of much of the cell’s macromolecular syntheses by one or more of the virus gene products, causing the death of the cell. Such an infection is said to be lytic. The mechanism of the shutoff varies among the viral families.  :IN SUMMARY, ALL VIRUSES are small; contain only one species of nucleic acid, either DNA or RNA; attach to their host cell with a specific receptor-binding protein; and express the information contained in the viral genome (DNA or RNA) using the cellular machinery of the host cell