Viral Genetics

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Information about Viral Genetics

Published on November 19, 2008

Author: salhas



Basic Virology Overview

VIRAL GENETICSSalwa Hassan Teama M.D.Molecular Biology Department/ Medical Research CenterAin Shams University/ Cairo/ Egypt Salwa Hassan Teama

Viruses??Salwa Hassan Teama 2012


VirusesObligate intercellular organismsCannot considered free-living Cannot reproduce outside of a living cell Salwa Hassan Teama

Viruses Affect virtually all life forms, including humans, animals, plants, fungi, and bacteria Often damage or kill the cells that they infect A few viruses can produce cancers Salwa Hassan Teama

Viruses Versus Cells Property Viruses CellsType of nucleic acid DNA or RNA but not both DNA and RNAProteins Few ManyLipoprotein membrane Envelope present in some Cell membrane present in viruses all cellsRibosomes Absent1 PresentMitochondria Absent Present in eukaryotic cellsEnzymes None or few ManyMultiplication by binary No Yesfission or mitosis1Arenaviruses have a few nonfunctional ribosomesTable adapted from Warren E. Levinson. Medical Microbiology and Immunology Salwa Hassan Teama

Viral Infections The most common cause of human disease Responsible for at least 60% of the illness Antibiotics have no effect on viruses, but antiviral drugs have been developed to treat life-threatening infections Vaccines that produce lifelong immunity can prevent viral infections Salwa Hassan Teama

Source: Wikipedia

Viral Infections Viruses in which the immune response eliminates them from the body (e.g. influenza and polio viruses). or Viruses can persist despite the host immune response. Salwa Hassan Teama

Persistent Viral InfectionsChronic carrier infections refer to people who produce viruslong periods of time and can serve as a source of infectionfor others (HCV).Latent infections are those infections can be reactivated at asubsequent time (Herpes).Slow virus infections are those infections with a longincubation period. Salwa Hassan Teama

Virus StructureViruses are particles composedof An internal core containingeither DNA or RNA (but notboth) covered by a protectiveprotein coat. Some viruses havean outer lipoprotein membrane,called an envelope, external tothe coat. Salwa Hassan Teama

Types of Viruses

Virus Structure Size & Shape Viral Nucleic Acids Viral Capsid and Symmetry Viral Proteins Salwa Hassan Teama

Size and ShapeViruses vary in size 20 to 300 nm in diameter.The shape of virus particles is determined by thearrangement of the repeating subunits that form theprotein coat (capsid) of the virus.Most viruses appear as spheres or rods in the electronmicroscope. In addition to these forms, bacterial virusescan have very complex shapes such as T4 phage. Salwa Hassan Teama

Size and Shape


BacteriophagesBacteriophages are viruses that invade bacteria.Examples include T4 and lambda, which infect E. coli.T4, multiplies by the lytic cycle which kills the host.Lambda, multiplies by the lysogenic cycle. It stays as aprophage until due to some trigger enters the lyticcycle. Salwa Hassan Teama

Viral Capsid and Symmetry The protein coat (capsid), made up of subunits called capsomers. The structure of the nucleic acid genome and the capsid protein is called the nucleocapsid. The arrangement of capsomers gives the virus structure its geometric symmetry. Three forms of symmetry either helical, icosahedral or complex. Salwa Hassan Teama

Viral Capsid and Symmetry Helical Icosahedral

Viral Nucleic Acids The viral nucleic acid is located internally. Single or double- stranded DNA or single or double- stranded RNA. The nucleic acid can be either linear or circular. The DNA is always a single molecule. The RNA exists either as a single molecule or in several pieces. Salwa Hassan Teama

Both influenza virus and rotavirus have a segmented RNA genome.

Viral Protein

The Outer Capsid Proteins Protect the genetic material, Mediate the attachment of the virus to specific receptors on the host cell surface, The major determinant of the species and organ specificity of the virus, Important antigens that induce neutralizing antibody and activate cytotoxic T cells to kill virus- infected cells. Salwa Hassan Teama

The Internal Viral Proteins Structural (e.g. the capsid proteins of the enveloped viruses), Enzymes. (e.g. the polymerases that synthesize the viral mRNA). Salwa Hassan Teama

Viral Envelope Some virus has an outer envelope. Lipoprotein membrane composed of lipid derived from host cell membrane and protein that is virus specific. Acquired as the virus exits from the cell in a process called budding. Derived from the cells outer membrane, except for herpes viruses acquired from the cells nuclear membrane. Salwa Hassan Teama

Enveloped Virus/ Non Enveloped VirusEnveloped Virus more sensitive to heat, drying,detergents and lipid solvents such as alcohol and etherthan non enveloped virus.Most often enveloped viruses transmitted by directcontact via blood and body fluids; others transmitted byrespiratory droplet. Most often non enveloped virusestransmitted by indirect means such as feco-oral route. Salwa Hassan Teama

Salwa Hassan Teama

The Baltimore Classification Source: Wikipedia

The Baltimore Classification Salwa Hassan Teama

DNA Viruses

Salwa Hassan TeamaSource: /

RNA Viruses

Salwa Hassan Teama

Retroviruses (Group VI) have a single-stranded RNA genome but aregenerally not considered RNA viruses because they use DNA intermediatesto replicate.

Virus ReplicationVirus Life Cycle

Virus Life CycleThe life cycle of virusesdiffers greatly betweenspecies but there are six basicstages: Salwa Hassan Teama

Virus Life CycleAttachment is a specific binding between viral capsid proteins andspecific receptors on the host cellular surface,Penetration; viruses enter the host cell through receptor- mediatedendocytosis or membrane fusion,Uncoating; the viral capsid is degraded by viral enzymes or hostenzymes thus releasing the viral genomic nucleic acid,Replication involves the synthesis of viral messenger RNA (mRNA (for viruses except positive sense RNA viruses,Assembly; viral protein synthesis and assembly of viral proteins andviral genome replication,Release viruses are released from the host cell by lysis. Envelopedviruses (e.g., HIV) typically are released from the host cell bybudding.

Virus ReplicationDNA virusesThe genome replication of most DNA viruses takes place in thecells nucleus.RNA virusesReplication usually takes place in the cytoplasm. RNA virusescan be placed into about four different groups depending on theirmodes of replication. RNA viruses use their own RNA replicaseenzymes to create copies of their genomes.Reverse transcribing viruses replicate using reverse transcription. Salwa Hassan Teama

Reverse Transcribing Viruses HIV HBV

Lytic and Lysogenic Cycles

Lysogenic Cycle Viral DNA merges with Cell DNA and does not destroy the cell. The Virus does not produce progeny. There are no symptoms of viral infection. Temperate viral replication takes place. Salwa Hassan Teama

Lytic Cycle Viral DNA destroys Cell DNA, takes over cell functions and destroys the cell. The Virus replicates and produces progeny phages. There are symptoms of viral infection. Virulent viral infection takes place. Salwa Hassan Teama

Viral Growth Curve

Salwa Hassan TeamaHost Virus Interaction Source:

Atypical Virus Like AgentsDefective viruses are composed of viral nucleic acid andproteins but cannot replicate without a helper virus whichprovides the missing function.Pseudovirions contain host cell DNA instead of viral DNAwithin the capsid.Viroids consist of a single molecule of circular RNA without aprotein coat or envelope.Prios are infectious particles that composed of proteins andcontain no detectable nucleic acid. Salwa Hassan Teama

Laboratory Diagnosis Identification of the virus in cell culture Microscopic identification directly in the specimen Serologic procedures to detect a rise in antibody titer or the presence of IgM antibody Detection of viral antigen in blood or body fluids Detection of viral nucleic acids in blood or patients cells Salwa Hassan Teama

Salwa Hassan Teama

Virus identification in cell culture Cytopathic (CPE) effect Hemadsorption/ Interference Complement fixation Hemagglutination inhibition Neutralization, Other procedure Fluorescent antibody assay ELISA RIA,…… Salwa Hassan Teama

Microscopic Identification  Electron Microscopy/ Immune electron microscopy; it detects virus particles, which can be characterized by their size and morphology.  Light microscopy; reveal characteristic inclusion bodies or multinucleated giant cell.  UV microscopy is used for fluorescent antibody staining of the virus in infected cells. Salwa Hassan Teama

Microscopic Identification

Detection of Viral AntigenAntigen detection Immunofluorescence ELISA etc………………………… Salwa Hassan Teama

Serology Antibody is detected in patients serum by reaction with known virus preparation (antigen); ELISA, RIA,.. The presence of IgM antibody can be used to diagnose current infection. The presence of Ig G antibody cannot be used to diagnose current infection. Rise in antibody titer that is 4 fold or greater in the convalescent serum sample compared to the acute sample can be used to make a diagnosis. Salwa Hassan Teama

Molecular Diagnostic Methods The gold standard method in viral diagnosis. Available since 1970s, when researchers began using cloned DNA probe to detect viral nucleic acid. Nucleic acid tests would rapidly replace traditional virus detection methods. Salwa Hassan Teama

Molecular Diagnostic MethodsThe goal is in the detection of Non culturable agents such as human papilloma virus, human parvovirus. Viruses difficult to culture, including enteric adenovirus, some coxsackie viruses. Viruses that are dangerous to culture such as HIV. Viruses that are present in low numbers, for example, HIV in antibody negative patients or CMV in transplanted organs.Salwa Hassan Teama

Molecular Diagnostic Methods Detect infections when a viable virus cannot be obtained (latent viral infection or viruses that are present in immune complexes). Predict antiviral drug susceptibilities. Differentiate antigenically similar viruses such as adenovirus types 40 and 41. Detect viral genotypes that are associated with human cancers (human papilloma virus). Salwa Hassan Teama

Laboratory Tests/ Sensitivity range Test % Sensitivity Range Rapid antigen Immunofluorescence assay 9-23% Enzyme immunoassay 0-20% Viral culture 20-45% RT-PCR 60-90% Serology Immunoglobulin M 58-81%Complement fixation> four fold rise 50%Enzyme immunoassay>four fold rise 85-95%

Viral Genetics Viruses grow rapidly Large number of progeny virions per cell More chances of mutations occurring over a short time period The nature of the viral genome (RNA/DNA; segmented/ non- segmented) plays an important role in the genetics of the virus DNA viruses tend to be more genetically stable than RNA viruses Error correction mechanisms in the host cell for DNA repair, but probably not for RNA Salwa Hassan Teama

Viruses undergo genetic change by severalmechanisms:Genetic drift where an individual bases in the DNA orRNA mutate to other bases.Antigenic shift is where there is a major change in thegenome of the virus. This occurs as a result ofrecombination. Salwa Hassan Teama

Salwa Hassan TeamaSource:

Source: www.

RecombinationProcess of exchange of genesbetween two chromosomes withinregions of significant base sequencehomology.This kind of break/joinrecombination is common in DNAviruses or those RNA viruses whichhave a DNA phase (retroviruses). Salwa Hassan Teama

Reassortment Non-classical kind of recombination. The mixing of the genetic material of a species into new combinations in different individuals. Virus has a segmented genome; RNA viruses e.g. orthomyxoviruses, reoviruses, arenaviruses,.. Novel reassortants Salwa Hassan Teama

Oncovirus A virus that can cause cancerViruses seem able to cause cancer in three ways Presence of the viral DNA may disrupt normal host DNA function. Viral proteins needed for virus replication may also affect normal host gene regulation. The virus may serve as a vector for oncogene insertion. Salwa Hassan Teama

Salwa Hassan TeamaSource:

References and Further ReadingWarren Levinson. Review of Medical Microbiology & Immunology: TenthEdition. 644 pages. McGraw Hill Professional, 2004. ISBN. 0071431993,9780071431996.Tristram G. Parslow , Daniel P. Stites , Abba I. Terr , John B. ImbodenMedical Immunology. Tenth Edition (March 23, 2001). 814 pages.McGraw-Hill/Appleton & Lange; ISBN-10: 0838563007ISBN-13: 978-0838563007Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World andevolution of cells. Biol. Direct. 2006;1:29.doi:10.1186/1745-6150-1-29. PMID 16984643.Parsonnet, Julie (1999). Microbes and malignancy: infection as a causeof human cancers. Oxford: Oxford University Press. ISBN 978-0-19-510401-1 Salwa Hassan Teama

THANK YOU Salwa Hassan Teama

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