MLS 316 Basic Microbiology PDF

BIOLOGY OF VIRUS Viruses come in an amazing variety of shapes and sizes. They are very small and are measured in nanometers, which is one-billionth of a meter. Viruses can range in their sizes between 20 to 400nm, which is 45,000 times smaller than the width of a human hair. Some filoviruses have...

BIOLOGY OF VIRUS Viruses come in an amazing variety of shapes and sizes. They are very small and are measured in nanometers, which is one-billionth of a meter. Viruses can range in their sizes between 20 to 400nm, which is 45,000 times smaller than the width of a human hair. Some filoviruses have a total length of up to 1400 nm; their diameters are only about 80 nm. The majority of viruses cannot be seen with a light microscope because the resolution of a light microscope is limited to about 200nm, so a scanning electron microscope is required to view most viruses. A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological classification. Viruses can have a lipid "envelope" derived from the host cell membrane. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The core of the virus is made up of nucleic acids, which then make up the genetic information in the form of RNA or DNA. Viruses are classified by factors such as their core content, capsid structure, presence of outer envelope, and how mRNA is produced. GENERAL CHARACTERISTICS OF VIRUSES  Viruses are much smaller than prokaryotic or eukaryotic cells (0.01-0.3um).  They have no metabolic system of their own.  They depend upon the machinery of the host cell for replication (obligate intracellular parasites).  They have either DNA or RNA genomes, but lack ribosomes and other factors needed for translation.  Their genomes encode minimal information to ensure the following: 1) Genome replication and packaging; 2) Production of viral proteins; and 3) Subvert cellular functions to allow the production of virions.  Some viruses destroy cells, producing disease; other persist in infected cells either in a latent or persistent state; and other may cause cellular malignant transformation.  Their shape varies from simple helical and icosahedral (polyhedral or near-spherical) forms to more complex structures with tides tails or an envelope.  Antibiotic have no effect on viruses, but antiviral drugs have been developed to treat life - threatening infection. Virus Characteristic Image created by Ben Taylor PHYSICAL PROPERTIES OF VIRUS 1. Size: The size of virus ranges from (20-300) nm in diameter. Parvovirus is the smallest virus with size 20nm whereas Poxvirus is largest being 400nm. 2. Shape: The overall shape of virus varies in different groups of virus. Most of animal viruses are spherical shape, Pox virus is rectangular shape, TMV is rod shape, Poliovirus is bullet shape etc. However, Some viruses are irregular and pleomorphic in shape. 3. Symmetry: Two basic symmetry are recognized in virus, they are either helical symmetry and icosahedral symmetry. In some virus, symmetry is more complex. 4. Resistance: i. Temperature: Most viruses are heat labile. Viruses are inactivated by heating at 60°C for 30 minutes or 100°C for few seconds. On the other hand, viruses are stable and resistant to cooling. Virus can be stored for long duration at -40°C to -70°C by lyophilization or freeze drying. ii. Radiation: Both non-ionizing and ionizing radiation can kill virus. Ultra violet rays causes pyrimidine dimer formation while ionizing radiation eg, X-rays causes lethal break of viral genome. iii. Organic solvent: Chloroform, ether and bile salt can destroy all viruses by lipid solubilization. iv. Disinfectant: Most viruses are destroyed by oxidizing agents such as chlorine, H 2O2, iodine etc. Many viruses are resistant to phenol and chlorination. The phenol and chlorine do not always inactivate enterovirus. 5. Metabolism: Viruses are metabolically inert outside host cell. They are thus called obligate intracellular parasite CHEMICAL PROPERTIES OF VIRUS i. Genome: Viral genome or nucleic acid contains either DNA or RNA but not both. The genome can be either ds DNA or ss DNA or ds RNA or ss RNA. The genome may be linear or circular. Most viruses possess linear genome except Papova virus which contains circular ss DNA. ii. Capsid: The Capsid is the outer shell of a virus. It protects the nucleic acid and also helps in attachments on host cell surface during infection. Structure of capsid gives the symmetry of virus. It forms the basis for classifying viruses into the four major groups. Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex. For example, the tobacco mosaic virus has a naked helical capsid. The adenovirus has an icosahedral capsid. iii. Envelope: Some viruses contain phospholipid bilayer known as envelope. It is acquired from host cell membrane. A virus lacking envelope is called naked virus. iv. Glycoprotein spike: The envelope of some virus contain spike-like projections called glycoprotein spike or peplomers. Glycoprotein spikes are an important antigenic structure. Neuraminidase and Haemagglutinin are glycoprotein spikes which help in virus attachment to cellular receptor on host cell to establish infection. v. Enzymes: Some viruses possess their own enzymes. Retrovirus possess reverse transcriptase  CLASSIFICATION/TAXONOMY OF VIRUS The international committee on taxonomy of virus (ICTV) has developed a uniform classification system. The committee places greatest weight on specific properties to define families: nucleic acid type, presence or absence of envelope, symmetry of capsid and dimensions of virion and the capsid. Although ICTV reports are the official authority on viral taxonomy, many virologists find it useful to group virsuses using a scheme devised by David Baltimore. The Baltimore system complements the ICTV system but focuses on the viral genome and the process used to synthesize viral mRNA. However, virus can be classified in a number of ways which includes: A] Classification on the basis of nucleic acid B] Classification on the basis of structure or symmetry C] Classification on the basis of replication properties and site of replication D] Classification on the basis of host range E] Classification on the basis of mode of transmission CLASSIFICATION BASED VIRUS STRUCTURE Viral nucleocapsids come in two basic shapes helical and icosahedral, although the overall appearance of a virus can be altered by the presence of an envelope, if present. Based upon basic morphology, there are five different basic structural forms of viruses. These forms are listed below with examples:  Naked helical - tobacco mosaic virus; no known human or animal viruses have this structure.  Enveloped helical - rhabdoviruses and paramyxoviruses.  Naked icosahedral - adenoviruses and picornaviruses.  Enveloped icosahedral - togaviruses and flaviviruses.  Complex - bacteriophages and poxviruses. Helical Viruses These viruses are composed of a single type of capsid subunits known as capsomere stacked around a central axis to form a helical structure, which may have a central cavity, or tube. This arrangement results in rod-shaped or filamentous virions. These can be short and highly rigid, or long and very flexible. The genetic material which is single-stranded RNA (ssRNA), but ssDNA in some cases, is bound into the protein helix by interactions between the negatively charged nucleic acid and positive charges on the protein. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it and the diameter is dependent on the size and arrangement of capsomeres. They are usually 15-19nm wide and range in length from 300 to 500nm depending on the genome size. However, the presence or absence of viral envelope differentiates this group of viruses into naked or enveloped helical. The well-studied tobacco mosaic virus is a naked helical virus while orthomyxoviruses and rhabdoviruses are example of enveloped helical virus. Icosahedral Viruses Most animal viruses are icosahedral or near-spherical with chiral icosahedral symmetry. The icosahedron is a polygon with 12 corners and 20 facets (sides) made up of equilateral triangles fused together in a spherical shape. The genetic material is fully enclosed inside of the capsid. The minimum number of identical capsomeres required for each triangular face is 3, which gives 60 for the icosahedron. Viruses with icosahedral structures are released into the environment when the cell dies, breaks down and lyses, thus releasing the virions. The most well-known examples of enveloped viruses are the togaviruses and flaviviruses while naked icosahedral viruses include adenoviruses and piconaviruses. Complex Viruses These viruses possess capsid that is either purely icosahedral or helical shape and may have a complex outer wall or head-tail morphology. The head-tail morphology structure is unique to viruses that only infect bacteria and are known as bacteriophages. The head of the virus has an icosahedral shape with a helical shaped tail. The bacteriophage tail acts like a molecular syringe to attach to the bacterium, creates a hole in the cell wall, and then inserts its DNA into the cell using the tail as a channel. The Poxvirus is one of the largest viruses in size and has a complex structure with a unique outer wall and capsid. One of the most famous types of poxvirus is the Variola virus which causes smallpox. Envelope Viruses These are conventional icosahedral or helical structures/viruses that are surrounded by a lipid bilayer membrane. The envelope is formed when the virus is exiting the host cell via budding, and the infectivity of this virus is mostly dependent on the envelope.. Virus envelope glycoproteins perform several functions, including the initial attachment of the virion to the target cell, penetration, fusion, and cell-to-cell spread, amongst others. The attachment of a virion to the cellular surface requires the envelope to be intact and the glycoproteins in their native conformation. Antiviral drugs that are directed against the envelope proteins can decrease the ability of the virus to attach and initiate infection, thereby decreasing infectivity. Generally, viruses are tolerant or sensitive to heat, detergents, solvents, alcohols e.t.c. Consequently, enveloped viruses mean they have outer lipid layer of glycoprotein and lipoproteins (envelop) that can be neutralized easily by various chemical and physical agents. The most well-known examples of enveloped viruses are the influenza virus, Hepatitis C and HIV. INTERNATIONAL COMMITTEE ON TAXONOMY OF VIRUS (ICTV) CLASSIFICATION OR CLASSIFICATION BASED ON NUCLEIC ACID The classification is dynamic in that new viruses are continuously being discovered and more information is accumulating about viruses already known. The basic viral hierarchical classification scheme is: Family - Subfamily - Genus - Species - Strain / Type. A number of viral characteristics, referred to below, define each of these taxonomic categories. Viruses are placed in families on the basis of many features. A basic characteristic is nucleic acid type (DNA or RNA) and morphology (that is, the virion size, shape, and the presence or absence of an envelope). The host range and immunological properties (serotypes) of the virus are also used. Physical and physicochemical properties such as molecular mass, density, thermal inactivation, pH stability, and sensitivity to various solvents are used in classification.  DAVID BALTIMORE CLASSIFICATION OF VIRUSES The Baltimore classification is a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), etc.) and their method of replication Group 1.dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses) Group II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses) Group III: dsRNA viruses (e.g. Reoviruses) Group IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g. Picornaviruses, Togaviruses) Group V: (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses) Group VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses) Group VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g. Hepadnaviruses) Group I: Double-stranded DNA viruses These types of viruses must enter the host nucleus before they are able to replicate. Furthermore, these viruses require host cell polymerases to replicate the viral genome and, hence, are highly dependent on the cell cycle. Proper infection and production of progeny requires that the cell be in replication, as it is during replication that the cell's polymerases are active. The virus may induce the cell to forcefully undergo cell division, which may lead to transformation of the cell and, ultimately, cancer. Examples include Herpesviridae, Adenoviridae, and Papovaviridae. There is only one well-studied example in which a class 1 virus is not replicating within the nucleus: the Poxvirus family, a highly pathogenic virus that infects vertebrates and includes the smallpox virus. Group II: Single-stranded DNA viruses Viruses in this category include the Anelloviridae, Circoviridae, and Parvoviridae (which infect vertebrates), the Geminiviridae and Nanoviridae (which infect plants), and the Microviridae (which infect prokaryotes). Most of them have circular genomes (the parvoviruses are the only known exception). Eukaryote-infecting viruses replicate mostly within the nucleus - usually via a rolling circle mechanism, forming double-stranded DNA intermediate in the process. A prevalent but asymptomatic human Anellovirus, called Transfusion Transmitted Virus (TTV), is included within this classification. Group III: Double-stranded RNA viruses As with most RNA viruses, this class replicates in the "Core" capsid, that is, in cytoplasm, not having to use the host replication polymerases to as much a degree as DNA viruses. This family is also not as well-studied as the rest and includes 2 major families, the Reoviridae and Birnaviridae. The virion contains RNA polymerase that transcribes each segment to mRNA. Group IV: Positive-sense single-stranded RNA viruses They replicate through a DNA intermediate. A well-studied family of this class of viruses includes the retroviruses. One defining feature is the use of reverse transcriptase to convert the positive-sense RNA into DNA. Instead of using the RNA for templates of proteins, they use DNA to create the templates, which is spliced into the host genome using integrase. Replication can then commence with the help of the host cell's polymerases. Group V: Single-stranded RNA viruses - Negative-sense The negative-sense RNA viruses and indeed all genes defined as negative-sense cannot be directly accessed by host ribosomes to immediately form proteins. Instead, they must be transcribed by viral polymerases into a "readable" form, which is the positive-sense reciprocal. These can also be divided into two groups:  Viruses containing non-segmented genomes for which replication occurs is within the cytoplasm and the first step in the replication is transcription from the (-)-stranded genome by the viral RNA-dependent RNA polymerase to yield monocistronic mRNAs that code for the various viral proteins.  Viruses with segmented genomes for which replication occurs in the nucleus and for which the viral RNA-dependent RNA polymerase produces monocistronic mRNAs from each genome segment. The largest difference between the two is the location of replication. Examples in this class include the families Arenaviridae, Orthomyxoviridae, Paramyxoviridae, Bunyaviridae, Filoviridae, and Rhabdoviridae (the latter of which includes the rabies virus). Group VII: Double-stranded DNA viruses They replicate through a single-stranded RNA intermediate. This small group of viruses, exemplified by the Hepatitis B virus (which is in the Hepadnaviridae family), have a double- stranded, gapped genome that is subsequently filled in to form a covalently closed circle (cccDNA) that serves as a template for production of viral mRNAs and a subgenomic RNA. The pregenome RNA serves as template for the viral reverse transcriptase for production of the DNA genome. REPRODUCTION IN VIRUS Since viruses are obligate intracellular microorganisms, they can only reproduce within their host cells utilizing the host cell machinery and metabolism. The parental virus (virion) gives rise to numerous progeny usually genetically and structurally identical to the parent virus. There are six basic stages in the reproduction/replication of a virus. Attachment: the virus attaches to the host cell membrane through interaction of viral proteins present on the capsid or phospholipid envelope with specific host cellular surface receptors. Penetration: the process of attachment to specific surface receptors can induce structural or conformational changes in viral capsid proteins or the phospholipid envelope which results in the fusion of the virion and cellular membrane. Uncoating: after the penetration of the host cell membrane, the viral capsid is removed and degraded by host cell enzymes (lysosomes) or viral viral enzymes releasing the viral genetic material or nucleic acid. Replication (Transcription or mRNA production): after the genome has been uncoated, transcription or translation of the viral genome is initiated. For positive sense RNA viruses, the infecting RNA genome is transcribed into messenger RNA (mRNA) while for negative stranded RNA and DNA, the genetic material is converted into complementary RNA. The mRNA is used to instruct the host cell to make virus components. The virus takes advantage of the existing cell structures to replicate itself. Synthesis of virus components: upon transcription, the virus continues to hijack the host’s organelles to synthesize its own components. The viral mRNA is translated on the host cell ribosomes into two types of viral proteins, structural and non-structural protein. New viral genome is synthesized from templates of parental genome or with single stranded nucleic acid and a newly formed complementary strand. Virion assembly: A virion is simply an active or intact virus particle. In this stage, the newly synthesized viral genome (nucleic acid) and proteins are assembled and packaged to form new virions that are ready for release from the host cell. This process can also be referred to as maturation. Virion release (liberation stage): The viruses now being matured are ready to be liberated from the host cell cytoplasm. There are two methods by which viruses are released from their host cell: lysis or budding. Lysis results in the death of an infected host cell and these viruses are referred to as cytolytic viruses. An example is seen in Variola major also known as smallpox. Enveloped virus such as influenza A virus are released from the host cell by gradual extrusion (budding). It is this process that results in the acquisition of viral phospholipid envelope. These types of viruses which do not usually kill the infected cell are termed cytopathic viruses. The new viruses may now invade or attack other cells or remain dormant in the cell. Most animal viruses are released without lysis. PATHOGENESIS OF VIRUS INFECTION Viral pathogenesis is simply the study of the interaction between viral and host factors, the processes and mechanisms by which viruses cause diseases in their target hosts often at cellular or molecular level. For infection to occur, the virus must hijack the host factors and evade the host immune response. A virus is pathogenic if it can infect and cause signs of disease in that host. Consequently, viral disease is a sum total of the effects of viral replication on/in the host cell and the host cell’s subsequent immune response against the virus. Steps in viral pathogenesis A. Host Entry and Primary replication: in order to establish an infection, a virus must first attach to and enter cells of its host. Virus can either attach to the skin, gastrointestinal tract, urogenital tract, respiratory tract or conjunctiva to begin a disease process. However, certain other viruses can be directly introduced into the blood stream either by needle prick or insect bite or by transmission from mother-to-child at the point of fertilization, child birth or via placenta. The frequency of implantation is usually greatest where the virus is directly in contact with living cells. Viruses usually replicate at the primary site of entry. Following successful entry into the host, the virus hijacks the host cell machinery to begin synthesis of its own amino acid/protein in order to multiply. The replicating virus must however, regulates the host immune response in order to prevent being eliminated by the body. Replicated virus from infected cells spread to infect adjacent healthy susceptible cells extracellularly or extracellularly. Intracellular spread occurs through fusion of infected cells with adjacent uninfected cells or by way of cytoplasmic bridges between cells. The establishment of infection at the portal of entry may be followed by continued local virus multiplication leading to localized disease or localized virus shedding. B. Dissemination (Viral spread) and Secondary Replication: After primary multiplication and spread at the sites of entry, viruses then spread within the host. The predominant mode of viral dissemination is via the circulatory system (bloodstream or lymphatic system). However, a minority of viruses can be spread through the nervous system. The presence of virus in the blood is called viremia. The virus carried in the bloodstream diffuses through the afferent lymphatics to the lymphoid tissues and then through the efferent lymphatics to infect cells in close contact with the bloodstream (endothelial cells). This initial spread may result in transient (primary) viremia. Subsequently release of the virus from the endothelial cells directly into the bloodstream induces a secondary viremia and this puts the virus in contact with the capillary system of all body tissues. The virus may diffuse into the target organ from the capillaries by replicating within the capillary endothelial cells or fixed macrophage and are being released on/in the target  organ. Infected cell may also reach the target organ via diffusion through small gaps in the capillary endothelium. The virus thus replicates and spread within the target organ site of excretion. Examples of viruses that spread through the bloodstream include chickenpox (varicella zoster virus), smallpox (variola) and HIV while rabies virus, herpes virus and poliovirus spread through the nerves. C. Cell Injury and Clinical illness: Viral multiplication in the target organ elicits several physiological alterations, cell injury and clinical illness in the host. This is because the local body defenses including interferon, local inflammation and local immunity are all activated. Circulating interferon and immune responses are responsible for the termination of viremia, but these responses may be too late to prevent the seeding of virus into the target organ and into sites of shedding. Depending on the balance between virus and host defenses, virus multiplication in the target organ may result in cell death. For example, the binding of HIV to co-receptors CCR5 or CXCR4 can trigger cell death. Other symptoms like malaise and anorexia may be as a result of diffusion of toxic products of viral replication and cell necrosis or due to the release of cytokines and other inflammatory mediators. The release of leukotriene C4 during respiratory infection may cause bronchospasm. More so, the impairment of leukocytes and immunosuppression may cause secondary bacterial infection. D. Viral shedding: The last stage in pathogenesis is the shedding of infectious virus into the environment. This is a necessary step to maintain a viral infection in populations of hosts. Shedding usually occurs from body surfaces involved in viral entry. Shedding represents the time at which an infected individual is infectious to contacts. However, in some viral infections such as rabies, humans represent dead end infections and shedding does not occur.