Introduction to Virology

Pathogenesis of Viral Diseases


Microorganisms – bacteria, protozoans & worms, fungi
- either single cells or composed of many cells

Cells – capable of independent replication
- can synthesize their own energy & proteins - can be seen in the light microscope Viruses – are not cells - not capable of independent replication - cannot synthesize own energy & proteins - too small to be seen in the light microscope

Capsid – protein shell, or coat, that encloses the nucleic acid genome Capsomeres - morphologic units seen in the electron microscope on the surface of icosahedral virus particles - represent clusters of polypeptides Defective virus – a virus particle that is functionally deficient in some aspects of replication Envelope – lipid-containing membrane that surrounds some virus particles - acquired during viral maturation by a budding process through a cellular membrane Peplomers – virus-encoded glycoproteins or projections exposed on the surface of the envelope Nucleocapsid – the protein-nucleic acid complex representing the packaged form of the viral genome Structural units – The basic protein building block of the coat - also called protomer Subunit – a single folded viral polypeptide chain Virion – the complete virus particle; serve to transfer the viral nucleic acid from one cell to another

mitochondria. external to the coat. called an envelope.particles composed of an internal core containing either DNA or RNA (but not both) covered by a protein coat. Some viruses have an outer lipoprotein membrane. not have a nucleus.Characteristics of Viruses 1) Viruses . . or ribosomes .

(-) mitochondria .(+) ribosomes  can synthesize own proteins . cytoplasm. mitochondria & ribosomes = prokaryotes –not divided into nucleus & cytoplasm .Cells both prokaryotic & eukaryotic – have both DNA & RNA = eukaryotic cells – have nucleus.

they do not undergo binary fission or mitosis . because they cannot generate energy or synthesize proteins  obligate intracellular parasites .vs. whereas one cell divides to produce only two daughter cells . chlamydiae & rickettsiae – cannot synthesize own energy to replicate independently 3) Viruses replicate in a manner different from that of cells .One virus can replicate to produce hundreds of progeny viruses.2) Viruses must reproduce (replicate) w/in cells.

Comparison of Viruses & Cells Property Viruses Cells Type of nucleic acid Proteins DNA or RNA but not both Few DNA and RNA Many Cell membrane in all Present Present in eukaryotes Many Lipoprotein membrane Envelope present in some Ribosomes Mitochondria Enzymes Absent Absent None or few Multiplication by binary fission or mitosis No Yes .

strandedness (single or double). type of symmetry. segments (number.Physicochemical properties of the virion – molecular mass. size & functional activities of structural & non-structural proteins. & presence or absence of membranes 2. & special functional activities. amino acid sequence. thermal stability & susceptibility to physical & chemical agents. esp. nucleotide sequence 3. . pH stability.Classification of Viruses Basis of classification 1. sense (positive. ether & detergents 4. whether linear or circular. buoyant density. shape.Virus genome properties – type of nucleic acid (DNA or RNA).Virion morphology – size. Virus protein properties – number. modifications. size of genome in kilobases or kilobase pairs. presence or absence of peplomers. negative or ambisense). size).

Paramyxovirus . genome structure. Genome organization & replication.. pathogenicity. Herpesviridae. Paramyxoviridae Genera . strategy of replication & cellular sites (virion assembly & release) 6. Antigenic properties 7.virus (physicochemical & serologic differences). tissue tropisms & pathology Families . mode of transmission. strategies of replication) . including gene order.-viridae (virion morphology. Biologic properties – natural host range. number & position of open reading frames.5. vectors relationships. Herpesvirus.

Containing Viruses Parvoviruses Polyomaviruses Papillomaviruses Adenoviruses Hepadnaviruses Herpesviruses Poxviruses .DNA.

gastroenteritis . 70-90 nm. 252 caps . & fetal death Polyyoma viruses – small.cubic symmetry.certain genotypes cause genital cancers Adenoviruses – medium sized. 32 capsomeres. 72 caps .Human parvovirus B 19  replicates in immature erythroid cells & causes several adverse consequences – aplastic crisis. cubic.JC virus – progressive multifocal leukoencephalopathy .BK virus – nephropathy in transplant patients Papillomaviruses – 55 nm .“wart viruses” . conjunctivitis. nonenveloped. fifth disease. nonenveloped. cubic symmetry. 45 nnm. 18-26 nm . no envelope .Parvoviruses – very small.acute respiratory diseases.

Epstein-Barr virus (inf mononucleosis). 40-48 nm.Hepadnaviruses – small.acute & chronic hepatitis. vaccinia. human herpesviruses 6 &7 (T lymphotropic) & human herpesvirus 8 (Kaposi sarcoma) Poxviruses – large brick-shaped or ovoid. cubic .varicella-zoster virus (chicken pox & shingles) .smallpox.all poxviruses tend to produce skin lesions . enveloped . 220-450 nm (L) x 140260 nm (W) x 140-260 nm thick .cytomegalovirus. lipid-cont envelope . molluscum contagiosum . 162 capsomeres. persistent infections associated w/ a high risk of developing cancer Herpesviruses – 150-200 nm.herpes simplex types 1 and 2 (oral and genital lesions) .

RNA-Containing Viruses Picornaviruses Arenavirus Astroviruses Coronaviruses Caliciviruses Retroviruses Hepeviruses Orthomyxoviruses Reoviruses Bunyaviruses Arboviruses Bornaviruses Togaviruses Filoviruses Paramyxoviruses Rhabdoviruses Flaviviruses Viroids Prions .

enteroviruses –(polioviruses.SARS Retroviruses – spherical. echoviruses .rotaviruses – gastoenteritis Arboviruses  have a complex cycle involving arthropods as vectors  transmit the viruses to vertebrate hosts by their bite .not a virus family.hepatovirus – hepatitis A Reoviruses – medium sized. ecologic grouping Coronaviruses .dengue. 28-30 nm. enveloped . cubic . 60-80 nm . enveloped.the viron contains a reverse transcriptase enzyme that produces a DNA copy of the RNA genome – HIV  AIDS .Picornaviruses – small. coxsackieviruses. encephalitis viruses . 80-110 nm in diameter .rhinoviruses – common colds .120-160 nm particles. yellow fever.

Structure Size & Shape = 20 to 300 nm in diameter = sphere. bullet. rod.determined by the arrangement of the repeating subunits that form the protein coat. bricks = complex structures of precise geometric symmetry = shape of virus particles . capsid .


HIV Influenza

Phage O29 Smallpox

Phage P22

Filamentous Phage Coronavirus

T4 Phage


Viral Nucleic Acids = viral nucleic acid (genome) – located internally - can either be single- or double-stranded DNA or single or double-stranded RNA - the NA can either be linear or circular

DNA – always a single molecule
RNA – can exist either as a single molecule or in several pieces Almost all viruses contain only a single copy of their genome

 haploid
Exception: Retrovirus family – members have two copies of their RNA genome  diploid

Capsid & Symmetry
Capsid – a protein coat which surrounds the nucleic acid - made up of subunits called capsomers - each capsomer consist of one or several proteins  E/M – spherical particle, w/ a central hole - the arrangement of capsomers gives the virus structure its geometric symmetry 2 forms of symmetry in viral capsids: 1. icosahedral – (cubic) capsomers are arranged in 20 triangles that form a symmetric figure (icosahedron) w/ the approx outline of a sphere

2. helical – capsomers are arranged in a hollow coil that appears rod-shaped The helix can be either rigid or flexible. Both the icosahedral & the helical forms can exist either as a “naked” nucleocapsid or with an outer envelope layer .

2. Outer viral proteins are also important antigens that induce neutralizing antibody & activate cytotoxic T cells to kill virus-infected cells. (after both natural infection & immunization) . = also the target of antibodies (antibodies bind to these viral proteins & prevent (“neutralize”) the virus from entering the cell & replicating.Viral Proteins Functions: 1. The outer capsid proteins – protect the genetic material & mediate the attachment of the virus to specific receptors on the host cell surface. This interaction of the viral proteins w/the cell receptor is the major determinant of species & organ specificity.

internal viral proteins = some are structural (capsid proteins of enveloped viruses) = Enzymes (polymerases that synthesize the viral mRNA) = Superantigens – produced by some viruses.retrovirus mouse mammary tumor virus . similar in their action to the superantigens of bacteria .herpesvirus family – Epstein-Barr virus & CMV .3.activation of CD4+ T cells is required for replication of these viruses to occur .

which attach to host cell receptors during the entry of the virus into the cell = matrix proteins – mediates the interaction between the capsid proteins & the envelope .found in the spike-like projections on the surface.Envelope = a lipoprotein membrane composed of lipid derived from the host cell membrane & protein that is virus-specific = glycoproteins .

Poliovirus types 1. 2. w/c are composed only of NA & capsid proteins The surface proteins of the virus. the presence of an envelope confers instability on the virus Enveloped virus are more sensitive to heat . & & lipid solvents such as alcohol & ether than are nonenveloped (nucleocapsid) viruses. 3 – distinguished by the antigenicity of their capsid proteins .In general. the capsid proteins or the envelope glycoproteins – the principal antigens against w/c the host mounts its immune response to viruses. They are also the determinants of type specificity (serotype) Ex. detergents.

Defective – NA & proteins but cannot replicate without a “helper” virus.Atypical viruslike agents 1.BSE – mad cow disease . Prions – infectious particles that are composed solely of proteins.scrapie . (-) NA = implicated as the cause of certain “slow” diseases called transmissible spongiform encephalopathies . w/c provides the missing function 2. can infect cells but they don’t replicate 3.Creutzfeldt-Jacob disease – humans . Pseudovirions – contain host cell DNA instead of viral DNA within the capsid.sheep . Viroids – consists solely of a single molecule of circular RNA without a protein coat or envelope 4.

= the time required for the growth cycle varies  it is minutes for some bacterial viruses and hours for some human viruses .Replication Viral Growth Curve = shows the amount of virus produced at different times after infection = presented in a typical growth curve  the amount of virus produced is plotted on a logarithmic scale as a function of time after infection.

ends with the appearance of virus (solid line) Latent period – the time from the onset of infection to the appearance of the virus extracellularly . there is alteration of cell morphology & marked derangement of cellular function Infection begins with one virus particle & ends with several hundred virus particles having been produced .First event – the disappearance of the virus (solid line dropping to the x axis) . the viral NA continues to function & begins to accumulate within the cell (dotted line) Eclipse period – the time during which no virus is found inside the cell .although the virus particle is no longer present .toward the end of this period.

synthesis of early proteins Viral genome replication Late viral mRNA synthesis  late viral protein synthesis Progeny virion assembly Virion release from cell .Stages of the viral growth cycle Attachment & penetration by parental virion Uncoating of the viral genome .viral DNA in the nucleus Early transcription – synthesis of early mRNA Early translation .

Viral Life Cycle .

A viral life cycle is dependent on a host cell .A virus will remain dormant until it is able to infect the next host.A virus needs to replicate & create progeny . activate & replicate .A virus cannot live on its own . create progeny. & spread to other hosts .Viruses use the most efficient method to locate a host.Inside a host – a virus’ sole purpose is to make as many copies of itself & infect other host cells .Active only when replicating within a host – using a host’s resources & food .Overview .

Viral infection occurs when a virus enters a host: * through a physical breach (cut in the skin) * direct inoculation (mosquito bite) * direct infection of the surface itself (inhalation of the virus onto trachea) It is only after a virus enters a host that it can gain access to possible susceptible cells .

Attachment or adsorption occurs between the viral particle & the host cell membrane  A hole forms in the cell membrane  then the virus particle or its genetic contents are released into the host cell  in the host cell viral reproduction may commence .Viral entry Virus must enter cells of the host organism – in order for it to reproduce & establish infection  use the cell’s materials Proteins found on the surface of the virus interact with proteins of the cell .

Viral replication A virus must take control of the host’s replication mechanisms A distinction between susceptibility & permissibility of a host cell is made Permissibility determines the outcome of the infection After control is established & the environment is set for the virus to begin making copies of itself. replication occurs quickly .

final stage in the viral life cycle .Viral Shedding -After a virus has made many copies of itself  exhaust the cell of its resources -Cell is no longer useful to the virus  must find new host Shedding – the process by which virus progeny are released to find new hosts .

Virus hide within another cell .evade the host cell defense or immune system .Viral latency .it is not the best interest of the virus to continually replicate -“hiding” – latency = virus will not produce any progeny = will remain inactive until external stimuli (light or stress) prompts it into activation .

Attachment or adsorption 2.Viral Entry . Viral Penetration . Entry pore formation 4. Membrane fusion or hemifusion state 3.virus comes into contact with the host cell & introduces viral material into the cell Major steps: 1.the earliest stage of the infection in the viral life cycle .

this attachment causes the two membranes to remain in mutual proximity.they have long tails on which to attach to receptors on the bacterial surface . influenza virus .Attachment or adsorption – receptors on the viral envelope become connected to complementary receptors on the cell membrane . Herpes simplex virus. favoring further interactions between surface points .enveloped viruses exhibiting this: HIV.non-enveloped viruses: bacteriophages or phages – virus that infect bacteria .this is also the first requisite that must be satisfied before a cell can become infected  makes the cell susceptible .

Membrane fusion or hemifusion state – the cell membrane is punctured & made to further connect with the unfolding viral envelope Entry pore formation – an opening is established for the stabilization of an opening for which viral particles can enter Viral penetration – viral capsid or genome is injected into the host cell’s cytoplasm .

HIV. Herpes simplex.the virus’ envelope blends with the cell membrane  releasing its contents .can be done only with viruses that contain an envelope .Entry via Membrane Fusion . influenza virus .viral receptors attach to the receptors on the surface of the cell & secondary receptors may be present to initiate the puncture of the cell membrane or fusion with the host cell  followed by the unfolding of the viral envelope .

inside the cell the virus breaks out of the vacuole to gain access to the cytoplasm .Examples: poliovirus. Foot-andmouth disease virus .Entry via Endocytosis .the virus tricks the cell into thinking that the virus knocking at the door is nothing more than nutrition or harmless goods . Hepatitis C virus.a cell takes in resources from the environment  attach goods into surface receptors  engulf them into the cell inside a vacuole .

Example: phages .restricted to viruses in which only the gene is required for infection of a cell (most all positive-sense. single-stranded RNA viruses .Entry via Genetic Injection . & inject only its gene into the cell.virus simply attaches to the surface of the cell via receptors on the cell. leaving the rest of the virus on the surface .

suppression of host cellular transcription & translation  cytotoxic effects  lead to the death & decline of a cell infected by a virus After the introduction of the viral particle unpacking of the viral proteins & the viral genome via some form of nucleic acid occurs as preparation for viral replication .suppression of cell signalling .suppression of intrinsic cell defenses ..Once a virus is in a cell  will activate formation of proteins to gain full control of the host cell .Control mechanisms include: .

Viral Replication .Formation of biological viruses during the infection process in the target host cells -Purpose: to allow production & survival of its own kind = by generating abundant copies of its genome & packaging these copies into viruses  to be able to continue infecting new hosts .Replication between viruses is greatly varied & depends on the type of genes involved .

RNA intermediat w/c acts as template for the production of (+) sense genomic RNA . flavivruses. & picornaviruses) – are termed plus sense or (+) sense – are translated by cellular ribosomes immediately after the entry of the genome into the cytoplasm Genome replication of (+) sense RNA-containing viruses requires the synthesis of a minus sense or (-) sense .Once a virus has entered a target cell  it must replicate its genome & proteins Replication strategies used by single –stranded RNA-containing viruses depend on whether the genome can be used as messenger RNA (mRNA) Translation-competent genomes (alphaviruses.

termed as the provirus .provirus is translocated to the nucleus & is integrated to the host chromosomal DNA .synthesis of the provirus is mediated by a virus.encoded RNA-dependent DNA polymerase or reverse transcriptase – so named because of the reversal of genetic information from RNA to DNA .stranded DNA copy.Retroviruses are RNA-containing viruses that replicate using a DNA intermediate = viral genomic RNA is (+) sense & single-stranded – -however does not serve as m-RNA = The retrovirus RNA genome is the template for the synthesis of a double.

Proper infection & production of progeny requires that the cell be in replication as that is when the cell’s polymerases are active .must enter the host nucleus before it its able to replicate . smallpox virus) .Example: Adenoviridae . (e.g.Poxvirus family – class I virus which does not replicate within the nucleus.requires host cell polymerases to replicate its genome – highly dependent on the cell cycle .Class 1: Double stranded DNA viruses .virus may induce the cell to forcefully undergo cell division  chronically this may lead to transformation of the cell  cancer .

Parvoviridae Class 3: Double stranded RNA viruses . Birnaviridae .do not use the host replication polymerases to as much degree as DNA viruses .Reoviridae.replication is monocistronic & includes individual.Circoviridae.replicate within the nucleus & form a double stranded DNA intermediate during replication .Class 2: Single stranded DNA viruses . segmented genomes – each of the genes code for only one protein .replicates in the cytoplasm as w/ most RNA viruses .

> viruses with complex transcription. ribosomal frameshifting & proteolytic processing of polyproteins may be used .can be directly accessed by host polymerases to immediately form proteins – two groups: > viruses where the genome RNA forms the mRNA & is translated into a polyprotein product that is subsequently cleaved to form the mature proteins.Class 4 & 5: Single stranded RNA viruses .two types = replication is primarily in the cytoplasm = replication is not as dependent on the cell cycle as other DNA viruses Class 4: Single stranded RNA viruses – positive (+) sense . for which subgenomic mRNAs. Flaviviridae.Examples: Coronaviridae. Picornaviridae .

Filoviridae & Rhabdoviridae .dependent RNA polymerase produces monocistronic m RNAs from each genome segment.Examples: Orthomyxoviridae. which is the positive sense reciprocal – two groups: > viruses containing non segmented genomes for which the first step in 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.Class 5: Single stranded RNA viruses – Negative (-) sense .cannot be directly accessed by host polymerases to immediately form proteins. Paramyxoviridae. . Replication is within the cytoplasm > viruses with segmented genomes for which replication occurs in the nucleus & for which the viral RNA. Bunyaviridae. A (+) sense genome copy is then produced that serves as template for the production of the (-) strand genome. Instead they must be transcripted by viral polymerases into a “readable form”.

gapped genome that is filled in to form a covalently closed circle (ccc DNA) that serves a a template for production of viral mRNAs & a subgenomic RNA.viruses have a double-stranded. The pregenomic RNA serves as template for the viral reverse transcriptase & for production of DNA genome = Example: Hepatitis B virus . which is spliced into the host genome using integrase  replication can then commence with the help of the host cell’s polymerases = Example: HIV Class 7: Double-stranded DNA viruses that replicate through a single stranded RNA intermediate .use reverse transcriptase to convert the positive sense RNA into DNA .use DNA to create templates of proteins (instead of using RNA).Class 6: Positive (+) sense single stranded RNA viruses that replicate through a DNA intermediate .

Viral Shedding .shedding from a single cell. from one part of the body to another part. and shedding from bodies into the environment where the viruses may infect other bodies = via budding = via apoptosis = via reverse endocytosis .refers to the successful production of virus progeny & that the progeny is leaving the cell to infect other host cells .

This process will slowly use up the cell membrane & eventually lead to the demise of the cell . smallpox .Prior to budding.“budding” through the cell envelope . the virus may put its own receptor on to the surface of the cell in preparation for the virus to bud through  forming an envelope with the viral receptors already on it .Via budding .use the cell’s membrane for the virus itself – most effective for viruses that need an envelope .this is also how antiviral responses are able to detect virus infected cells = Examples: HSV. SARS.

Via apoptosis . before apoptotic bodies of dead cell material clump off the cell to be absorbed by macrophages.way for a virus to get into macrophages either to infect them or simply travel to other tissues in the body .primarily used by non-enveloped viruses but enveloped viruses may also use this = HIV – enveloped virus that exhibits this process for the infection of macrophages . .cell suicide  release of progeny into the extracellular space .usually controlled  results in the cell’s genome being chopped up.

Via reverse endocytosis .used primarily by non-enveloped viruses. although enveloped viruses may do this too = Example: use of recycling viral particles in the enveloped Varicella-Zoster virus .viral progeny are synthesized within the cell & the host cell’s transport system is used to enclose vacuoles of virus progeny for release into the extracellular space .

proviral .the ability of a pathogenic virus to lie dormant within a cell. denoted as the lysogenic part of the viral life cycle . virus production ceases.the virus can reactivate & begin producing large amounts of viral progeny without the host being infected by new outside virus – stays within the host indefinitely .Viral latency .Mechanisms: episomal.a phase in certain viruses’ life cycles in which after initial infection. however the the viral genome is nor fully eradicated .

Advantages: > the virus does not need to enter the nucleus & hence may avoid ND10 domains from activating interferon via that pathway > far easier to maintain & reactivate than proviral latency .more vulnerable to marauding ribozymes or host foreign gene degradation than provirus latency .viral genes are floating in the cytoplasm or nucleus as distinct objects .Disadvantages: more exposure to cellular defenses  leading to possible degadation of viral gene via cellular enzymes .Episomal latency .refers to the use of genetic episomes during latency .Herpesviridae – Herpes simplex virus – undergoes episomal latency in neuron cells & leaves genetic material floating in the cytoplasm .

Example: Retroviruses HIV  the nucleus inserts its gene between Long Terminal Repeats using integrase & remains within the host own gene .begins when the virus genome integrates into the host genome  becomes a provirus .Advantages: automatic host cell division results in replication of the viruses’ gene .requires that the viral gene get into the nucleus & insert itself into the host genome .Disadvantages: include the need to enter the nucleus & increased difficulty in maintaining the latency .Proviral latency .


Fusion inhibitor . Others – Amantadine & rimantadine .acyclovir.Nucleoside Analogs – inhibit NA replication by inhibition of polymerases for NA replication .cidofovir 3.saquinavir 5.foscarnet INTERFERON – host-coded proteins that are members of the large cytokine family which inhibit viral replication .Nucleotide – attached phosphate group . Protease inhibitors . Nonnucleoside Reverse transcriptase inhibitor . disrupt catalysis .Antiviral Agents 1. lamivudine.blocks the virus & cellular membrane fusion step 6. zidovudine 2.binds directly to reverse transcriptase.nevirapine 4.

Viral Vaccines Killed-Virus Vaccines Attenuated Live-virus vaccines Table 30-9 .

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