Virology An Introduction

Virology: An introduction Introduction Viruses have predatory nature  Viruses can cause a variety of diseases from common cold and the flu to serious illnesses such as AIDS, dengue fever, measles, small pox and bird flu.  All viruses infect cells and hijack the host cellular machinery for their own benefit.  Learning about the biology and structure of viruses can help us better understand the diseases that they cause, their prevention and treatment.  Viruses have shaped the history and evolution of their hosts, like humans, animals and plants as they are affected by viral infections  medical consequences of Viral infections of humans have altered the history of mankind (e.g. corona virus)  Virtually all living organisms have viral parasites including bacteria.   Virus particles have evolved to transfer genetic material between cells and to encode information sufficient to ensure their own continued propagation.  Viral particles are made from protein codes and nucleic acid pores  so we can say: the virus is a genome and a productive protein code  Regarding to effect ,viruses are extracellular organelles.  The status of viruses wether they are living or inactive agents is still under huge debate  They contain most or all of the molecular machinery necessary for efficient and specific packaging of viral genomes, escape from an infected cell, survival of transfer to a new host cell, attachment, penetration, and initiation of a new replication cycle. In many cases, the molecular machinery works in part by subverting more elaborate elements of the host cell apparatus for carrying out related processes.  The principles of virus structure thus arise from the requirements imposed by the functions of viral molecular architecture. There is more biological diversity within viruses than in all the rest of the bacterial, plant, and animal kingdoms put together ,and this is the result of the successful viruses in parasitizing all non-groups of living organisms Viruses are submicroscopic obligate intracellular parasites that differ from all other organisms:* Virus particles are produced from the assembly of preformed components where as the agents grow from an increase in the integrating some of there components and they produce by division, There particles themselves don’t grow or undergo division  • Viruses lack the genetic information for generation of metabolic energy for protein synthesis, they lack ribosomes, outside the cell, viruses are nearly complex th simplage of metabolically innered chemicals • Viruses inside cells behave like living organisms while outside them they are inactive complex chemicals (opinio of some virologists) • Molecular investigation of certain infectious agents has further complications • The number of novel pathogenic entities possess properties which can found the definition of viruses, they are clearly more similar to viruses than other organisms, these entities are known as prions and viroids  Viroids Very small Circular RNA molecules (200-400 nt) with a rod-like secondary structure. They have no capsid or envelope and are associated with certain plant disease, they different from viruses that they lack the protective protein coat (capsid)  Virusoids Satellite, viroid - like molecules,(1000 nt ) packaged into virus capsids as passengers.  Prions Infectious agents generally believed to consist of a single type of protein molecule with no nucleic acid component, confusion arises from the fact that prion protein and gene which encodes it are also found in the normal non infected cell The Origin of virology  Virology is a “ new” discipline in biology and it’s as far as the pharmatic recognitional viruses that is distinct form from other living organisms.  Not only Ancient people were aware of the effects of virus infection, but in some instances are also carried out active research into a cause and prevention of a virus disease  1400 BC: A hieroglyph from Memphis depicts a temple priest showing clinical signs of paralytic poliomyelitis.  1196 Bc: The Pharoh Ramses V is believed to have succumbed to smallpox because he has blisters.  Viral diseases were discovered much earlier before the discovery of the causative agents of these disease (120130 years before)  Perhaps the first written record of virus infection consists of hieroglyph of the capital of ancient Egypt made in 400 BC, which shows the clinical signs of a certain disease.  Henle was the first to propose the existence of viruses in 1840.  Failure of Henle Koch postulates to explain all cases paved the way to discover viruses.  19th /20th century: The concept of filtrable agents developed.  1909: The first demonstration of a virus being a cause of human disease by Landsteiner and Popper who showed that poliomyelitis was caused by a filtrable agent. 1939: The first electron micrograph of a virus tobacco mosaic virus (TMV) followed by the demonstration of many filtrable agents from animals and humans,  the term “virus” in latin terms refers to slimy liquid or poison .   1949: Isolation of viruses in cell culture.  Later years witnessed the elucidation of both the structure and chemical composition of viruses.  In the 1950’s and 1960’s there was an explosion in the discovery of new viruses.  Prompted by a rapidly growing mass of data, several individuals and committees independently advanced classification schemes which led to confusion and controversy.  In summary Viruses are commonly defined as “ the smallest (20-300 nm) infectious agents that are obligate intracellular parasites, contain either DNA or RNA and depend on the biochemical machinery of living cells to copy themselves, they’re hugely variable.”  Viruses cannot be regarded as microorganisms for they are not cells, they have no ribosomes, mitochondria or other organelles, and are metabolically inert.  Virus Structure   Virus particles form regular geometric shapes even though the proteins which viruses are made are irregularly shaped And they come in a great variety of shapes and sizes. Structural features are determined by requirements for assembly, exit, transmission, attachment and other functions of viruses. Virus Structure    Size: 17 nm – 3000 nm diameter Basic shape – Rod-like or “Spherical” Capsid :Protective protein Shell that surround the viral nucleic acid: – Made of many identical protein subunits – Symmetrically organized – 50% of weight • Enveloped or non-enveloped Virus Structure • Genomic material: nucleic acid of the virus, it can be: – – – – DNA or RNA Single- or double-stranded Circular or linear RNA can be positive or negative sense Structures compared From Medical Microbiology, 5th ed., Murray, Rosenthal & Pfaller, Mosby Inc., 2005, Fig. 6-4.  Viral structural components include:Capsid : The protein shell directly surrounding viral nucleic acid (coat, shell). Composed of capsomeres.  Genome : Nucleic acid of the virus ( RNA or DNA).  Nucleocapsid : the complete protein – nucleic acid complex.  Envelope: The lipid bilayer and associated glycoproteins that surround some viruses.  Virion: The entire infectious virus particle.  VIRUS STRUCTURE    Basic rules of virus architecture, structure, and assembly are the same for all families Some structures are much more complex than others, and require complex assembly and disassembly The capsid (coat) protein is the basic unit of structure; functions that may be fulfilled by the capsid protein are to: – – – – – – Protect viral nucleic acid Interact specifically with the viral nucleic acid for packaging Interact with vector for specific transmission Interact with host receptors for entry to cell Allow for release of nucleic acid upon entry into new cell Assist in processes of viral and/or host gene regulation Capsid symmetry and Virus Architecture  Virus capsid must be made up of multiple protein molecules (subunit construction) and viruses must overcome the problem of how these subunits are arranged.  It was demonstrated that when mixtures of purified virus nucleic acid and coat proteins were incubated together, virus particle formed.     Stability is an important feature of the virus particle, some viruses are fragile (unable to survive outside the protected host cell environment), many are able to survive for a long period (for years in some cases) The forces, which drive assembly of virus particles,include hydrophobic and electrostatic interactions. Only rarely are covalent bonds involved in holding together the multiple subunits. In biological terms, this means that protein – protein, protein – nucleic acid, and protein – lipid interactions are used. Capsid symmetry and virus architecture   Capsid consists of a homeoprotein molecule which as it fall to assume it’s mature conformation, it traps the virus genome inside. In practice, this arrangement can’t occur because: the triplet nature of the genetic code means that 3 nucleotides for double strand genomes are necessary to encode one amino acid. Viruses can’t utilize an alternative genetic code because this could not be deciphered by the host cell since the approximate molecular weight of a nucleotide triplet is 1000 and the average molecular weight of a single amino acid is 150, a nucleic acid can only encode protein (usually) that is 50% of it’s weight, therefore virus capsid must be made up of multiple protein molecules viruses must overcome a problem that is: how can we arrange protein subunits? It was demonstrated that when mixtures of purify nucleic acid and coat proteins were connected together so virus particles are formed, virus particles could form continuously from purified subunits without any extraneous information indicates that the particle was in the free energy minimum and the favored state was formed of the component Helical Capsids   The simplest way to arrange multiple identical protein subuints is to use the rotation symmetry and to arrange the irregularly shape of the protein around a circumference of a circle to form a desk, multiple desks form a cylinder, this cylinder coats the virus genome Close examination of helical viruses revealed that the structure of the capsid actually consists of a helix rather than a pile of stacked disks.  Some helices are rigid, but some helical viruses demonstrate considerable flexibility and longer helical viruses are often curved or bent.  Flexibility is important, long helical particles are likely to bent so they are less able damage  Helical naked animal viruses do not exist. All, however, have a similar design (- ss RNA and basic structural features). Icosahedral (Isometric) capsids     Hollow quasi spherical structure enclosing the genome within them, it’s arrangement is more complex than helical capsid. An Icosahedron is a solid shape consisting of 20 triangular faces arranged around the surface of a sphere. It has 12 vertices and 30 edges. Since protein molecules are irregularly shaped and are not regular equilateral triangles, the simplest icosahdral capsids are built up by using three identical subunits to form each triangular faces. This means that (60) identical subunits are required to form a complete capsid. Icosahedral Symmetry   12 vertices 20 faces (equilateral triangles)   5-3-2 symmetry axes 60 identical subunits in identical environments can form icosahedral shell What is an Icosahedron? Icosahedron: a geometric solid with twenty faces. Each face is an equilateral triangle and every vertex of the icosahedron is formed by five triangular faces. Edges 30; Vertices 12; Faces 20 Complex structure  Such viruses often consist of several layers of protein and lipid.  The larger and more complex viruses can not be simply defined by a mathematical equation, like icosahedral and helical capsids Because of complexity, they have defied attempts to determine detailed atomic structures using the techniques used for viral studies.  Enveloped viruses  Viruses have devised strategies to effect an exit from the infected cell without its total destruction.  Viruses leaving the cell must allow cell membrane to remain intact. This is achieved by extrusion (budding) of the particle through the membrane  The envelope may be acquired from intracellular structures. Enveloped Viruses ( membrane lipids, proteins, glycoproteins that is usually derived from the plasma membrane of the infected cell ) Properties  Environmentally labile, disrupted by acid, detergents, drying and heat  Modify cell membrane during replication  Released by budding Followed by cell lysis in some cases Consequences  Cannot survive in the GI tract  Must stay wet(Spread in large droplets, secretions, and organ transplants or blood transfusion.) Need not kill the cell to spread  Initiate a CMIR (Pathogenesis is often due to hypersensitivity and inflammation initiated by CMI)   Viruses modify their lipid envelope with several classes of proteins: o Matrix proteins Internal virion proteins that link nucleocapsid to envelope. o Glycoproteins Transmembrane proteins of two types: External glycoproteins ( spikes).  Transport channel proteins They enable the virus to alter permeability of the membrane( M2 of influenza) . Naked Viruses (protein) Properties   Environmentally stable to drying , heat, acid, protease and detergents Consequences Can be spread easily ( fomites, hand, dust,etc…..)   Can dry out and retain infectivity  Can survive adverse conditions in the gut.  Resist poor sewage treatment  Can elicit a protective antibody response Released from infected cells by lysis  Lysis: releasing viruses from the infected cell when it dies  This strategy sometimes is wasteful resulting in the premature death of the cell, it also reduces the possibilities infection  Therefore, many viruses have other strategies that they effect and exit without destroying it, the difficulty of this method that cells have lipid bilayer  The viability of the cell depends on the integrity of it’s membrane, viruses leaving the cell must therefore allow the membrane to remain in tact , this is achieved by the budding of the particles through the membrane, so the particle become coated in a lipid envelope derived from the host cell membrane with a simillar composition.  The envelope may be acquired from intracellular structures.  In the surface of the virus discovered only with this layer wouldn’t permit recognition of receptor molecules on host cells  Viruses therefore modify the lipid in the loop with several classes of proteins (e.g. matrix proteins which are internal proteins whose function is to link the nucleocapsid to the envelope) these are most abundant and unglycosylated  Glycoproteins (proteins with sugar) are two types: 1) external glycoproteins like the spikes 2) Internal glycoproteins  Transport channel proteins enable the virus to altered permeability of the membrane  Transport channel proteins are important to modify the internal environment of the virion driving biochemical changes necessary for maturation of the particle and the development of the infectivity (e.g. M2 of influenza)  The presence of an envelope significantly effects virion as following: 1. for naked viruses: they’re environmentally stable for drying, heating , proteasing detergents Genomes   The proposition and structure of virus genomes are more vary than any other creature The genome may be DNA or RNA (never both as genome is composed only of a single type of nucleic acid), SS (single stranded) (usually DNA)or ds (double stranded) (usually RNA) , in a linear, circular or segmented configuration (e.g. Influenza)    Single – stranded virus genomes may be either (+) Sense having the same polarity of nucleotide sequence as mRNA, (-) sense or ambience (usually access template for production of the positive sense) Genome size ranges from 3500 nucleotides (there are smaller in fact as the genome of some defective viruses 1700 nucleotides) to 470000 (235 KPB) nucleotides. The Physical nature of nucleic acid dictates the strategy of replication and forms a basis for classification. Viral genomes DNA viruses ss DNA ds DNA RNA viruses + ss RNA - ss RNA RNA   DNA viruses ss RNA ds DNA (Retroviruses) (hepadnaviruses) genome can function as mRNA • genome is template for mRNA • genome is template for DNA synthesis ("retrovirus") • Effects of Physical and chemical Agents    Vital dyes Neutral red, toluidine blue and Proflavin (bind to the nucleic acid and deactive the virus) Photodynamic inactivation: some viruses are refractory penetration by these dyes but they incorporate them in incubation in dark so visruses are inactive. Proteolytic enzymes Pronase inactivates viruses whereas GI enzymes( trypsin, chemotrypsin, and pepsin) are inefficient. Ether and chloroform Inactivate enveloped viruses.   Detergents, iodine, chlorine, and alcohol: Variable effects. Phenol: Most viruses are relatively stable.  PH: All viruses are stable at a pH of 5 to 9.  Salts and glycerol: Stabilize viruses. Classification of Viruses  Different       Bases Type of nucleic acid Size and morphology Presence of an envelope Effect of Ether Clinical Epidemiology