Introduction to VirologyIntroduction to Virology

Brief History, Viral Structure and Brief History, Viral Structure and Classification, and Role of Host Classification, and Role of Host

Cells in Viral InfectionsCells in Viral Infections

Smallpox (Variola Virus) – 10th Smallpox (Variola Virus) – 10th Century B.C.Century B.C.

Records of epidemics in AsiaRecords of epidemics in Asia Highly infectiousHighly infectious Often fatal (15 – 45% fatality)Often fatal (15 – 45% fatality)

Smallpox (Variola Virus) -Smallpox (Variola Virus) -10th Century B.C.10th Century B.C.

Variola, “spot” – vesicular rashVariola, “spot” – vesicular rash Chinese prevent infection by self-Chinese prevent infection by self-

inoculation of pus from lesionsinoculation of pus from lesions Termed “variolation”Termed “variolation”

Smallpox – 18th CenturySmallpox – 18th Century

Dr. Edward Jenner (England)Dr. Edward Jenner (England) Similar infection in cowsSimilar infection in cows Milkmaids infected by cowpox do not get Milkmaids infected by cowpox do not get

smallpoxsmallpox

Used the pus from cowpox lesions to Used the pus from cowpox lesions to inoculate and prevent smallpoxinoculate and prevent smallpox

Termed “vaccination” (vaccinus, cow)Termed “vaccination” (vaccinus, cow)

Smallpox – 20th CenturySmallpox – 20th Century

Use of chick embryo, tissue/cell culture Use of chick embryo, tissue/cell culture to study virus in the labto study virus in the lab

Research & Development for Biological Research & Development for Biological Warfare (USA, Soviet Union)Warfare (USA, Soviet Union)

Smallpox – 20Smallpox – 20thth Century Century

1967 - World Health Organization 1967 - World Health Organization (WHO) begins program to vaccinate (WHO) begins program to vaccinate susceptible personssusceptible persons

1977 – last natural case of disease in 1977 – last natural case of disease in BangladeshBangladesh

1979 – WHO declares smallpox 1979 – WHO declares smallpox eradicatederadicated

Smallpox – 21Smallpox – 21stst Century Century Vaccinia virus / Canarypox virus expression Vaccinia virus / Canarypox virus expression

vectors are used for experimental live vectors are used for experimental live recombinant virus vaccines recombinant virus vaccines

Smallpox – 21Smallpox – 21stst Century Century

FEAR and concern of its possible use as a FEAR and concern of its possible use as a bioterrorism weapon arisebioterrorism weapon arise

Tobacco Mosaic Virus (TMV)Tobacco Mosaic Virus (TMV)

Iwanowski (Russia in 1892) – found that Iwanowski (Russia in 1892) – found that after bacteria are removed by filtration of the after bacteria are removed by filtration of the sap, the sap remains infectioussap, the sap remains infectious

Stanley (USA) – crystallized TMV from plant Stanley (USA) – crystallized TMV from plant extractextract

TMVTMV

Electron microscopy reveals that the virus is Electron microscopy reveals that the virus is a rod shaped, helical particlea rod shaped, helical particle

Bacterial VirusesBacterial Viruses

Twort & d’Herelle (1915) – infected Twort & d’Herelle (1915) – infected bacterial colonies become “clear,and bacterial colonies become “clear,and watery” and are killed; agent was watery” and are killed; agent was termed bacteriophage (bacteria-eating)termed bacteriophage (bacteria-eating)

Bacterial VirusesBacterial Viruses

Delbruck & Luria (1952)–Delbruck & Luria (1952)–Performed genetic studies Performed genetic studies using plaque assaysusing plaque assays(more on this later)(more on this later)

Lwoff – reported on infections where there is no cell Lwoff – reported on infections where there is no cell lysis, and where the viral genome is incorporated lysis, and where the viral genome is incorporated into the host DNA (lysogenic / latent infection)into the host DNA (lysogenic / latent infection)

RNA Tumor VirusesRNA Tumor Viruses

Rous (USA, 1911) – reported Rous (USA, 1911) – reported that a virus infection of that a virus infection of chickens resulted in sarcomachickens resulted in sarcoma

Related viruses were Related viruses were shown to cause leukemiashown to cause leukemia in cats, mice, and cowsin cats, mice, and cows

RNA Tumor VirusesRNA Tumor Viruses

Identified as Retroviruses (RNA to DNA)Identified as Retroviruses (RNA to DNA)

DNA Tumor VirusesDNA Tumor Viruses

Shope (USA) – shows that a DNA virus is Shope (USA) – shows that a DNA virus is responsible for papilloma in rabbitsresponsible for papilloma in rabbits

DNA Tumor VirusesDNA Tumor Viruses

Related viruses were found in mice, cows, horses, Related viruses were found in mice, cows, horses, and primatesand primates

The Virus:Host interactions of these viruses were The Virus:Host interactions of these viruses were used as a model to study cell regulationused as a model to study cell regulation

Human Papilloma Virus

Emerging InfectionsEmerging Infections

Emerging VirusesEmerging Viruses

Ebola Virus - Ebola Virus - fatal hemorrhagic fatal hemorrhagic feverfever

HIV – HIV – chronic infection,chronic infection,

immune deficiencyimmune deficiency

Emerging VirusesEmerging Viruses Hantavirus – hemorrhagic fever Hantavirus – hemorrhagic fever + pulmonary infection+ pulmonary infection

Prion – proteinaeous infectious particle Prion – proteinaeous infectious particle causing subacute spongiform causing subacute spongiform encephalopathy encephalopathy

Emerging VirusesEmerging Viruses

West Nile Virus –West Nile Virus – asymptomatic,asymptomatic, encephalitis (1%)encephalitis (1%)

Severe Acute Severe Acute Respiratory Syndrome Respiratory Syndrome (SARS) (SARS)

Emerging VirusesEmerging Viruses

Avian Influenza virus (H5, N1) – Avian Influenza virus (H5, N1) – fatal pneumoniafatal pneumonia

Introduction to VirologyIntroduction to Virology What is a virus?What is a virus?

Extremely smallExtremely small SubmicroscopicSubmicroscopic Must use an electron microscope to “see”Must use an electron microscope to “see” Passes through filters used to “sterilize” solutionsPasses through filters used to “sterilize” solutions

Obligate, intracellular parasitesObligate, intracellular parasites Can’t be cultured on artificial mediaCan’t be cultured on artificial media

Variation in virus sizeVariation in virus size

What is a virus?What is a virus? Biochemically viruses are similar to, but different from “living organisms”Biochemically viruses are similar to, but different from “living organisms”

Both viruses and other living organisms contain proteins and Both viruses and other living organisms contain proteins and glycoproteinsglycoproteins

While other living organisms contain both RNA and DNA, viruses contain While other living organisms contain both RNA and DNA, viruses contain either DNA or RNAeither DNA or RNA, but not both, but not both

DNA viruses DNA viruses may be linear with open or closed ends,may be linear with open or closed ends, circular (closed or nicked),circular (closed or nicked), single stranded, or single stranded, or double strandeddouble stranded

RNA virusesRNA viruses may be linear single stranded, may be linear single stranded, segmented single stranded, or segmented single stranded, or segmented double stranded segmented double stranded If single stranded, the strand may be of either the plus or the minus sense (more If single stranded, the strand may be of either the plus or the minus sense (more

later on this)later on this)

Types of viral nucleic acidTypes of viral nucleic acid

What is a virus?What is a virus? Unlike other living organisms, viruses contain no polysaccharides, Unlike other living organisms, viruses contain no polysaccharides,

small molecules or ionssmall molecules or ions Other living organisms contain lipids. Lipids, if found in viruses, are Other living organisms contain lipids. Lipids, if found in viruses, are

only found in enveloped viruses (more on this later on)only found in enveloped viruses (more on this later on) Viruses lack the genetic information that encodes the apparatus Viruses lack the genetic information that encodes the apparatus

necessary for the generation of metabolic energy or for protein necessary for the generation of metabolic energy or for protein synthesissynthesis

The growth curves of viruses are very different from those of other The growth curves of viruses are very different from those of other organisms:organisms:

Growth curves of bacteria (A) Growth curves of bacteria (A) versus bacteriophages (B)versus bacteriophages (B)

Differences in growth curves:Differences in growth curves: Virus particles are produced from the assembly of pre-Virus particles are produced from the assembly of pre-

formed components: other organisms grow from an formed components: other organisms grow from an increase in the integrated sum of their components and increase in the integrated sum of their components and reproduce by cell division.reproduce by cell division.

Viruses don’t “grow” or undergo divisionViruses don’t “grow” or undergo division There are six basic phases in the multiplication cycle of all There are six basic phases in the multiplication cycle of all

virusesviruses AttachmentAttachment PenetrationPenetration UncoatingUncoating BiosynthesisBiosynthesis AssemblyAssembly ReleaseRelease

The multiplication cycle of a virusThe multiplication cycle of a virus

One step growth curveOne step growth curve

A one-step growth curve of bacteriophage λ following infection of susceptible bacteria (Escherichia coli). During the A one-step growth curve of bacteriophage λ following infection of susceptible bacteria (Escherichia coli). During the eclipse phase(1), the infectivity of the cell-associated, infecting virus is lost as it uncoats; during the maturation eclipse phase(1), the infectivity of the cell-associated, infecting virus is lost as it uncoats; during the maturation phase(2) infectious virus is assembled inside cells (cell-associated virus), but not yet released; and the latent phase(3) phase(2) infectious virus is assembled inside cells (cell-associated virus), but not yet released; and the latent phase(3) measures the period before infectious virus is released from cells into the medium. Total virus is the sum of cell-measures the period before infectious virus is released from cells into the medium. Total virus is the sum of cell-associated virus +released virus. Cell-associated virus decreases as cells are lysed. This classic experiment shows that associated virus +released virus. Cell-associated virus decreases as cells are lysed. This classic experiment shows that

phages develop intracellularly.phages develop intracellularly.

What is a virion?What is a virion? A A virionvirion is a structurally complete virus that is a structurally complete virus that

is capable of infecting new cellsis capable of infecting new cells

Structure of viruses:Structure of viruses: Composed of nucleic acid (either DNA or RNA)Composed of nucleic acid (either DNA or RNA) Surrounding the nucleic acid is a protein outer Surrounding the nucleic acid is a protein outer

coat (a coat (a capsidcapsid) which is composed of units called ) which is composed of units called capsomerscapsomers which are formed by the association of which are formed by the association of individual proteins called individual proteins called protomers. protomers. The capsid :The capsid : Functions to protect the delicate inner nucleic acid from Functions to protect the delicate inner nucleic acid from

physical, chemical or enzymatic damage.physical, chemical or enzymatic damage. May function in attachment of the virus to the host cell.May function in attachment of the virus to the host cell. May provide enzymes essential for virus entryMay provide enzymes essential for virus entry Functions to ensure that the virus genome is released Functions to ensure that the virus genome is released

only at the appropriate time and locationonly at the appropriate time and location

Capsomers, continuedCapsomers, continued The arrangement of the capsomers determines The arrangement of the capsomers determines

the architecture of the virus or the the architecture of the virus or the nucleocapsidnucleocapsid (composed of nucleic acid and the capsid). (composed of nucleic acid and the capsid). There are two basic types of capsomer There are two basic types of capsomer arrangements:arrangements: HelixHelix

Looks like a hollow tube or cylinder with the nucleic acid Looks like a hollow tube or cylinder with the nucleic acid inside. inside.

The proteins are arranged around the circumference of a The proteins are arranged around the circumference of a circle to form a disc. circle to form a disc.

Multiple discs are stacked on top of each other. Multiple discs are stacked on top of each other. The helix may be rigid or flexible.The helix may be rigid or flexible.

Helical StructureHelical Structure

Helical structureHelical structure

Capsid architecture continuedCapsid architecture continued IcosahedralIcosahedral

Looks like a sphere, but it actually has Looks like a sphere, but it actually has 20 triangular 20 triangular faces and 12 cornersfaces and 12 corners made by the intersection of 5 made by the intersection of 5 faces. faces.

For small viruses, each face (capsomer) consists of For small viruses, each face (capsomer) consists of three structural subunits (protomers). three structural subunits (protomers).

The faces of larger viruses are made from The faces of larger viruses are made from multiples multiples of three subunitsof three subunits..

Icosahedral architectureIcosahedral architecture

Icosahedral architectureIcosahedral architecture

Capsid architecture continuedCapsid architecture continued Some viruses are more complex and don’t Some viruses are more complex and don’t

fit into either architectural type.fit into either architectural type.

PoxvirusPoxvirus

ReovirusReovirus

Structure of Viruses, continuedStructure of Viruses, continued The nucleocapsid of many viruses is The nucleocapsid of many viruses is

surrounded by an envelope. surrounded by an envelope. The envelope is derived from host cell The envelope is derived from host cell

membranes. membranes. Viruses differ as to which host cell membrane is Viruses differ as to which host cell membrane is

used for their envelope, i.e., plasma membrane, used for their envelope, i.e., plasma membrane, Golgi, endoplasmic reticulum (E.R.), or nuclear Golgi, endoplasmic reticulum (E.R.), or nuclear membranes may be used. membranes may be used.

Enveloped virusesEnveloped viruses

Sindbis virus: an enveloped icosahedron

Enveloped virusesEnveloped viruses

Influenza A virus (an orthomyxovirus) and vesicular stomatitis virus (a rhabdovirus): viruses with enveloped helical structures. Although their morphology is different, these viruses are constructedin the same way.

Structure of Viruses, continuedStructure of Viruses, continued Viruses without an envelope are called Viruses without an envelope are called naked naked

viruses. viruses. Enveloped virusesEnveloped viruses have an advantage in that they have an advantage in that they

may exit the host cell without destroying it. may exit the host cell without destroying it. For example, viruses that use the host cell plasma For example, viruses that use the host cell plasma

membrane as the envelope, may take part of the host membrane as the envelope, may take part of the host cell plasma membrane as the viruses exit the cell (a cell plasma membrane as the viruses exit the cell (a process called process called buddingbudding) and the host cell membrane ) and the host cell membrane reseals itself. (More detail will be provided on this reseals itself. (More detail will be provided on this process later in the quarter)process later in the quarter)

BuddingBudding

Enveloped virusesEnveloped viruses Enveloped viruses modify their lipid envelopes by Enveloped viruses modify their lipid envelopes by

directing the synthesis of different classes of virally directing the synthesis of different classes of virally encoded proteins that are specifically transported encoded proteins that are specifically transported to and associated with the membrane that to and associated with the membrane that eventually becomes their envelope.eventually becomes their envelope. Matrix proteinsMatrix proteins – bind to the inner surface of the – bind to the inner surface of the

membrane to link the nucleocapsid to the membrane in membrane to link the nucleocapsid to the membrane in the assembly process.the assembly process.

Glycoproteins Glycoproteins – are transmembrane proteins. External – are transmembrane proteins. External glycoproteins have large ectodomains and small glycoproteins have large ectodomains and small endodomains. Monomers of these proteins often endodomains. Monomers of these proteins often associate to form multimers and may function in:associate to form multimers and may function in:

Enveloped virusesEnveloped viruses Receptor bindingReceptor binding Fusion, a process that takes place during entry of the Fusion, a process that takes place during entry of the

virus into the host cell (more on this later)virus into the host cell (more on this later) Transport channel proteins Transport channel proteins

May span the membrane several times. May span the membrane several times. May be important for modifying the internal May be important for modifying the internal

environment of the virus by altering membrane environment of the virus by altering membrane permeability.permeability.

Types of viral proteins associated Types of viral proteins associated with the envelopewith the envelope

Influenza virus

Structural Roles of Host Cells in Structural Roles of Host Cells in Viral InfectionsViral Infections

In order for a virus to successfully infect a In order for a virus to successfully infect a host cell, the cell must contain the host cell, the cell must contain the receptor receptor that the virus binds to in the process of that the virus binds to in the process of initiating an infection.initiating an infection. Receptors on animal cells are found on the Receptors on animal cells are found on the

plasma membrane. plasma membrane. They may be proteins, glycoproteins, or glycolipids.They may be proteins, glycoproteins, or glycolipids. Many viruses bind to the carbohydrate side chains of Many viruses bind to the carbohydrate side chains of

glycoproteins.glycoproteins.

Receptors on animal cellsReceptors on animal cells

Structural Roles of Host Cells in Structural Roles of Host Cells in Viral InfectionsViral Infections

In order for a virus to successfully infect a In order for a virus to successfully infect a host cell, the host cell must:host cell, the host cell must: Contain the receptor for the virus, Contain the receptor for the virus, It must also have the It must also have the cellular machinerycellular machinery that the that the

virus needs for replication. virus needs for replication. Differences in the organization of the cell’s Differences in the organization of the cell’s

genome and how it carries out the processes of genome and how it carries out the processes of replication, transcription and translation play an replication, transcription and translation play an important role in virus replication. important role in virus replication.

Eukaryotic cellsEukaryotic cells Several linear chromosomes; diploidSeveral linear chromosomes; diploid No operons; each gene is regulated by its No operons; each gene is regulated by its

own controlling elememts; monocistronic own controlling elememts; monocistronic mRNA (rare IRES sites)mRNA (rare IRES sites)

Post-trascriptional modification of RNAPost-trascriptional modification of RNA SplicingSplicing Addition of 5’capAddition of 5’cap Addition of 3’ poly A tailAddition of 3’ poly A tail

Eukaryotic cells, continuedEukaryotic cells, continued Internal compartmentalizationInternal compartmentalization

Nucleus for replication and transcriptionNucleus for replication and transcription Cytoplasm for translationCytoplasm for translation

Once cells differentiate, they exit the cell Once cells differentiate, they exit the cell cycle.cycle.

Classification of VirusesClassification of Viruses There are various ways to classify viruses:There are various ways to classify viruses:

On the basis of diseaseOn the basis of disease On basis of the host organismOn basis of the host organism On basis of virus particle morphologyOn basis of virus particle morphology On the basis of viral nucleic acidOn the basis of viral nucleic acid The most commonly used classification scheme is the Baltimore The most commonly used classification scheme is the Baltimore

scheme. This scheme is based on the relationship between the scheme. This scheme is based on the relationship between the viral genome and the mRNA used for translation during viral genome and the mRNA used for translation during expression of the viral genome:expression of the viral genome:

Class I = double stranded DNA virusesClass I = double stranded DNA viruses Class 2a= single stranded + sense DNA (DNA has the same Class 2a= single stranded + sense DNA (DNA has the same

sequence as the mRNA, except T replaces U)sequence as the mRNA, except T replaces U) Class 2b= single stranded – sense DNA (The DNA is complementary Class 2b= single stranded – sense DNA (The DNA is complementary

to the mRNA)to the mRNA)

The Baltimore Classification of The Baltimore Classification of VirusesViruses

Class 3= double stranded RNAClass 3= double stranded RNA Class 4= single stranded + sense RNA (the genome Class 4= single stranded + sense RNA (the genome

sequence is the same as the mRNA and can often be sequence is the same as the mRNA and can often be directly translated into protein product)directly translated into protein product)

Class 5= single stranded – sense RNA (the RNA is Class 5= single stranded – sense RNA (the RNA is complementary to the mRNA and thus, the genomic complementary to the mRNA and thus, the genomic RNA cannot be directly translated into a protein product)RNA cannot be directly translated into a protein product)

Class 6= single stranded + sense RNA that requires Class 6= single stranded + sense RNA that requires synthesis of a double stranded DNA molecule for the synthesis of a double stranded DNA molecule for the expression of the genome (retroviruses)expression of the genome (retroviruses)

Class 7 = this is a new class for viruses termed Class 7 = this is a new class for viruses termed reversiviruses which replicate their double stranded reversiviruses which replicate their double stranded DNA genome via a positive sense single stranded RNA DNA genome via a positive sense single stranded RNA intermediateintermediate

Baltimore Classification of VirusesBaltimore Classification of Viruses