Introduction to viruses

What are VirusesA virus is a non-cellular particle made up of genetic material and protein that can invade living cells.

The Structure Of a VirusViruses are composed of a core of nucleic acidThe Nucleic acid core is surrounded by a protein coat called a capsidThe Nucleic core is either made up of DNA or RNA but never both

RetrovirusChange DNA into RNA.Example of a Retrovirus is HIV

A typical, "minimal" retrovirus consists of: an outer envelope which was derived from the plasma membrane of its host many copies of an envelope protein embedded in the lipid bilayer of its envelope a capsid; a protein shell containing two molecules of RNA and molecules of the enzyme reverse transcriptase

WHAT IS A VIRUS?

Viruses may be defined as acellular organisms whose genomes consist of nucleic acid, and which obligately replicate inside host cells using host metabolic machinery to different extents, to form a pool of components which assemble into particles called virions.F A virus differs from a cell in three fundamental ways:iA virus usually has only a single type of nucleic acid serving as its genetic material. This can be single or double stranded DNA or RNA;iiViruses contain no enzymes of energy metabolism, thus cannot make ATP;iiiViruses do not encode sufficient enzymatic machinery to synthesize their component macromolecules, specifically, no protein synthesis machinery.

Fundamentally then, a virus is:A package of genetic information protected by a protein shell for delivery into a host cell to be expressed and replicated

Viruses are distinguished from other obligate parasites, some of which are even simpler than viruses:MYCOPLASMA: Small bacterium that grows only in complex medium or attached to eucaryotic cells.CHLAMYDIA: Obligate intracellular bacterial parasite which depends on eucaryotic cell for energy.PROTOZOA: Obligate intracellular parasite that replicate within eucaryotic cells.

VIROID: Infectious agents of plants that exist as naked nucleic acid (circular single stranded (ss) ssRNA).

HEPATITIS DELTA VIRUS (HDV): Viroid-like agent whose replication is dependent upon HBV.

Viral diseases have played a major role in human history over whatever time scale we choose to explore:

Over the past 1000 years: Smallpox and measles were brought to North and South America by early European explorers/conquerers. These diseases, for which the native American populations had no acquired partial immunity, killed large fractions of the populations, and were a major factor in the decimation of these societies.

Over the past 10 years: As the global HIV epidemic continues, sporadic cases and outbreaks in humans of some non-human host viruses such as Ebola and Hanta raise the concern about future epidemics by other viruses in the new century. FourCorners Virus (Hanta)

PREVENTING CONTROLING CURING VIRAL DISEASES

Smallpox: effective vaccine; this is the only viral disease that has been wiped out worldwide

Measles: effective vaccine since 1963; this disease could be eliminated with a world-wide effort

Influenza: effective strain-specific vaccine, but new variant strains emerge periodically

Polio: effective vaccine; will soon be the second viral disease wiped out

HIV: no vaccine; effective drugs, but they are costly and toxic, plus resistant strains appear. World-wide spread continues via intimate contact. 50 million infected thus far

Ebola: no vaccine; important host species unknown (found recently in chimps and rodents); outbreaks controllable because people die quickly and human-human transmission is via blood

Hanta: no vaccine; rodent host; easy transmission to humans, but outbreaks controllable

How are viruses classified ?

Hierarchical virus classification: (order) family - subfamily - genus - species - strain/type

All families have the suffix viridae, e.g.:

*Poxviridae *Herpesviridae *Parvoviridae *Retroviridae

Genera have the suffix virus. Within the Picornaviridae there are 5 genera:

*enterovirus (alimentary tract), species e.g. poliovirus 1, 2, 3 *cardiovirus (neurotropic), species e.g. mengovirus *rhinovirus (nasopharyngeal region), species e.g. Rhinovirus 1a *apthovirus (cloven footed animals ), species e.g. FMDV-C *hepatovirus (liver), species e.g. Hepatitis A virus

Virus naming and classificationUsually based on data available at the time of discovery:

iDisease they are associated with, e.g.:Poxvirus, Hepatitis virus, HIV, measles virus

iiCytopathology they cause, e.g.:Respiratory Syncytial virus, Cytomegalovirus

iiiSite of isolation, e.g.:Adenovirus, Enterovirus, Rhinovirus

ivPlaces discovered or people that discovered them, e.g.:Epstein-Barr virus, Rift Valley Fever

vBiochemical features, e.g.:Retrovirus, Picornavirus, HepadnavirusRSV

These naming conventions can lead to confusion later, e.g., viral hepatitis is caused by at least 6 different viruses * 10-20% of cases of presumed viral hepatitis are still not accounted for

Thus,Different viruses can cause (nearly) the same symptoms. e.g., the hepatitis viruses

However, different members of the same group can cause different symptoms. e.g., the herpes viruses

HerpesvirusesHSVHerpes Simplex VirusCold sores (type 1), Genital lesions (type 2)VZVVaricella Zoster VirusChicken poxCMVCytomegalovirusMononucleosisEBVEpstein-Barr VirusMononucleosis, Burkitts lymphoma, Nasopharyngeal carcinomaand HHV-6, HHV-7, HHV-8.. (Human HerpesVirus-#)

Virus Classification is now based principally on analysis of the particle:

Morphology:by electron microscopy Serology: antigenic cross-reactivity Genetic material: form of nucleic acid ssDNA (+ or - strand) dsDNA ssRNA (+ or - strand) dsRNA segmented RNA genetic organization sequence homology DNA sequence Hybridization

FamilyPoxHerpesAdenoPapovaParvoHepadnaGenome

ssDNAPartial dsDNACapsidsymmetryComplex

Envelope

Yese.g.Vaccinia virusHerpes simplexvirus 2HumanadenovirusPapilloma Hepatitis BAdeno-AssociatedMolluscumContagiosumAnimal virus classification: DNA Viruses

Plus Sense RNA Viruses

Plus-sense RNA viruses

Family

Corona

Toga/Flavi

Picorna

Calici

Retro

Genome

Diploid (+) RNA

Capsid symmetry

Helical

Envelope

Yes

e.g.

Human corona virus

Rubella virus

Hepatitis C virus

Polio

Hepatitis A virus

Norwalk agent

Hepatitis E virus

HIV-1

Minus Sense RNA Viruses

Minus-sense RNA viruses

Family

Paramyxo

Rhabdo

Filo

Orthomyxo

Arena

Bunya

Reo

Genome

ss(-) RNA segments

ss(+) or (+/-)

segments

ss(+) or (+/-)

segments

ds RNA

segments

Capsid symmetry

Icosahedral

Envelope

No

e.g.

Measles

Mumps

Para-influenza

Rabies virus

Ebola virus

Influenza virus

Lassa virus

Hanta virus

Rotavirus

The tiniest viruses are 20 nm in diameter. (smaller than a ribosome)

They consist of nucleic acids enclosed in a protein coat and sometimes a membranous envelop.

The genomes (sets of genes) maybeDouble stranded DNASingle stranded DNADouble stranded RNASingle stranded RNAThey are called either a DNA or RNA virus depending on the type of nucleotide in the make-up.They may be linear or circularThe smallest have only 4 genes and largest have several hundred.

Capsid a protein shell that covers the viral genome. They may beRod-shapedPolyhedralMore complex

Capsids are built from large numbers of protein subunits called CAPSOMERESThe most complex capsids are found in viruses that infect bacteria BACTERIOPHAGES (T1-T7)They have a protein tail piece with tail fibers that attach to the bacterium

Virus structure, classification and replication

From Medical Microbiology, 5th ed., Murray, Rosenthal & Pfaller, Mosby Inc., 2005, Fig. 6-4. Structures compared

Basic virus structureCapsid proteinNucleocapsidNaked capsid virus=+NucleocapsidLipid membrane, glycoproteinsEnveloped virus+

Capsid symmetryIcosahedralHelicalNaked capsidEnveloped

Properties of enveloped virusesEnvelope is sensitive toDryingHeatDetergentsAcidConsequencesMust stay wet during transmissionTransmission in large droplets and secretionsCannot survive in the gastrointestinal tractDo not need to kill cells in order to spreadMay require both a humoral and a cellular immune responseAdapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA Box 6-5

Properties of naked capsid virusesCapsid is resistant toDryingHeatDetergentsAcidsProteasesConsequencesCan survive in the gastrointestinal tractRetain infectivity on dryingSurvive well on environmental surfacesSpread easily via fomitesMust kill host cells for release of mature virus particlesHumoral antibody response may be sufficient to neutralize infectionAdapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA , Box 6-4

Summary: structure,classification & replicationStructureNucleic acid in a protein shell, +/- lipid envelopeStructure impacts on biological propertiesClassificationMany virus families, organized by structure and biologyReplicationGeneric schemeVarying strategies depending on nucleic acid

ReproductionViruses are obligate intracellular parasites that can reproduce only within a host cell.They do not haveEnzymes for metabolismDo not have ribosomesDo not have the equipment to make proteins

Each type of virus can infect and parasitize only a limited range of host cells called its HOST RANGE.Some are broad based while others are not.Swine flu virus can infect swine or humansRabies can infect may mammalsSome can parasitize only E. coliEukaryote viruses are usually tissue specificViruses use a lock and key fit to identify hosts.

Reproduction occurs using lytic or lysogenic cyclesThe Lytic CycleCulminates in the death of the host cellVirulent viruses reproduce only by lytic cyle.Natural selection favors bacterial mutations with receptor sites that are resistant to a particular phage or that have restriction enzymes to destroy the phages.The Lysogenic CycleReplication of the viral genome without destroying the host cell.A temperate virus may reproduce by either cycle. Lambda virus: resembles T4 but only has a single short tail fiber

RETROVIRUSESMost complicatedGenetic information flows in the reverse directionHave the enzyme reverse transcriptaseTranscribes DNA from an RNA templateThe newly made DNA than integrates as a provirus into the nucleus of the animal cellThe hosts RNA polymerase transcribes the virual DNA into RNA molecules.

Viral DiseasesThe damage caused by a viral disease depends on the ability of the tissue infected to regenerate by cell division.Cold virus we recover fromPoliovirus - attacksVaccines are harmless variants of pathogenic microbes that stimulate the immune system to defenses against the pathogen.

The link between viral infection and the symptoms it produces is often obscure.Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from lysosomes.Some viruses cause the infected cell to produce toxins that lead to disease symptoms.Other have molecular components, such as envelope proteins, that are toxic.In some cases, viral damage is easily repaired (respiratory epithelium after a cold), but in others, infection causes permanent damage (nerve cells after polio).

The first vaccine was developed in the late 1700s by Edward Jenner to fight smallpox.Jenner learned from his patients that milkmaids who had contracted cowpox, a milder disease that usually infects cows, were resistant to smallpox.In his famous experiment in 1796, Jenner infected a farmboy with cowpox, acquired from the sore of a milkmaid with the disease.When exposed to smallpox, the boy resisted the disease.Because of their similarities, vaccination with the cowpox virus sensitizes the immune system to react vigorously if exposed to actual smallpox virus.Effective vaccines against many other viruses exist.

Vaccines can help prevent viral infections, but they can do little to cure most viral infection once they occur.Antibiotics which can kill bacteria by inhibiting enzyme or processes specific to bacteria are powerless again viruses, which have few or no enzymes of their own.Some recently-developed drugs do combat some viruses, mostly by interfering with viral nucleic acid synthesis.AZT interferes with reverse transcriptase of HIV.Acyclovir inhibits herpes virus DNA synthesis.

In recent years, several very dangerous emergent viruses have risen to prominence.HIV, the AIDS virus, seemed to appear suddenly in the early 1980s.Each year new strains of influenza virus cause millions to miss work or class, and deaths are not uncommon.The deadly Ebola virus has caused hemorrhagic fevers in central Africa periodically since 1976.Fig. 18.8a

Transmission of VirusesRespiratory transmissionInfluenza A virusFaecal-oral transmissionEnterovirusBlood-borne transmissionHepatitis B virusSexual TransmissionHIVAnimal or insect vectorsRabies virus

Acute Virus InfectionsLocalised to specific site of bodyDevelopment of viraemia with widespread infection of tissues

PoliovirusEnterovirus.Possesses a RNA genome.Transmitted by the faecal oral route.Cause of gastrointestinal illness and poliomyelitis.Properties of the virus

Poliovirus InfectionNon-neuronaltissues

Incidence of PoliomyelitisPoliovirus vaccinesA: Salk killed inactivated vaccine.B: Sabin live attenuated vaccine

Influenza A virusMyxovirusEnveloped virus with a segmented RNA genomeInfects a wide range of animals other than humansUndergoes extensive antigenic variationMajor cause of respiratory infectionsProperties of the virus

Influenza A virus InfectionSpread by respiratory routeVirus infects cells of the respiratory tractDestruction of respiratory epitheliumSecondary bacterial infectionsAltered cytokine expression leading to fevere.g interleukin-1 and interferon

Spread of influenza virus

Respiratory Tract

ANTIGENIC DRIFTANTIGENIC SHIFTGeneration of Novel Influenza A Viruses

Viruses and Human TumoursEpstein Barr VirusBurkitts LymphomaHuman papillomavirusBenign wartsCervical CarcinomaHuman T-cell Leukaemia Virus (HTLV-1)LeukaemiaHepatitis C virusLiver carcinoma

Virus-induced tumours

Virus-Induced TumoursVirus infects cell.Virus nucleic acid, as DNA, integrates into cellular genome.Virus causes changes in cellular gene expression.Uncontrolled cell multiplication and tumour formation.

Source of infection:

Routes of entry:sexual

vertical transmission

Some viruses can cross the placentaInfection during pregnancy can damage the foetus

e.g. Rubella, Cytomegalovirus

Infection during first trimester:

Congenital infection syndrome:cataractsheart defectsmicro-cephaly mental retardationdeafnessRubella:

Disease determined by cell tropism:localiseddisseminated

After entry into the body:Viral infections can be localised, to the site of inoculation e.g.Human papillomaviruses - skin (warts)

or the body surface

e.g. RotavirusInfantile gastro-enteritis

Respiratory tract

e.g. InfluenzaVirus replicates and is shed from the body surface, highly infectious

occurs via the blood (viraemia) or lymphatic systemviruses may travel free in the plasma but usually hitch a ride with monocytes or lymphocytesa few viruses can spread via the nervous system eg. rabies Dissemination.

Some examples of generalised viral infections:

Measles

Viral haemorrhagic feverzoonosis

Rabies

How do viruses cause disease?

by damaging/killing cells outright by inducing immuno-pathology by transforming cells

. by damaging/killing cellse.g.Poliomyelitisthe virus is cytolyticdestroys motor neurons in the spinal cord, and so causes paralysisX-section of the spinal cord showing severe inflammation of anterior horn cells

. by inducing immunopathologyThe patients T cells attack and destroy virus-infected cellsInflammation and cell death

Help!

T cell

by transforming cells cancer

When a virus infects a cell, it expresses proteins that cause the cell to proloferate and/or block apoptosis

Cancer is multi-factorial: Oncogenic viruses are very common, only a small % of people infected actually get cancer

Major viral cancersCopyright John Valentine DMD 1999Cancer of the cervixCancer of the liverCertain leukaemias & lymphomasKaposis sarcoma

Viruses are involved in about 15% of human cancers:

+++++++++++++B Latency:e.g. herpes simplex virus

Classification of Human VirusesFields Vriology (2007) 5th edition, Knipe, DM & Howley, PM, eds, Wolters Kluwer/Lippincott Williams & Wilkins, Philadelphia Table 2.1

Major diseases caused by human viruses

These two lectures will review some features of viruses from the basic virology to the development of immunity to virus infections.2 As with many infections viruses can be transmitted between susceptible individuals by a variety of means. The details provided related mainly to viruses infecting humans. Many animal viruses do not remain infectious for very long outside the host. Respiratory: Influenza A virus (and rhinovirus). Transmission in the form of aerosols during coughing and sneezing. The viruses are fairly sensitive to drying and their transmission is highest when individuals are in close contact. Faecal-oral: Enteroviruses (e.g. poliovirus) A lot of viruses are excreted in faeces following high levels of replication in the gut. Blood borne: Hepatitis B (and HIV). Transferred through contaminated blood products or via shared needles with drug abuse. Sexual transmission: (HIV)Animal/insect vector: Rabies. In many instances the virus infection is a specific pathogen of the animal and is not normally transmitted to humans by any other means. The spread of virus during acute virus infection can be variable with two general patterns: Localised to specific site of body: The virus infects at a specific site of the body and does not spread beyond that site - i.e. little or no viraemia.Development of viraemia with widespread infection of tissues: The virus can infect at one site in the body but develops a viraemia with extensive spread beyond the initial entry to cause a number of diverse disease symptoms. Enterovirus.Possesses a RNA genome.Transmitted by the faecal oral route.Cause of gastrointestinal illness and poliomyelitis.

The main features of an enterovirus infection are as follows: The virus is transmitted by the faecal oral route and is ingested from contaminated food or water - the contamination of these sources is due to the excretion of virus in the faeces of an infected individual. The initial site of infection is the gut and in the majority of cases (ca 90% for poliovirus) the virus does not spread further and the infection may be inapparent. The virus can spread beyond the initial site of infection as a viraemia with virus spread via the blood and lymph. During the viraemia the virus can infect tissues beyond the initial site of entry - e.g. non-neuronal tissues (heart for CBV) as well as neuronal tissues.Enteroviruses are an important cause of aseptic meningitis and in the case of neuronal infections by poliovirus there can be severe paralysis leading to fatalities. The incidence of poliovirus is declining and is due for complete eradication in the next 5-10 years.This has been achieved by the use of two vaccines for poliovirus.Salk Vaccine: The first to be produced. This is a killed vaccine in which the virus is no longer able to replicate but it can still act as an antigen to stimulate an immune response in the vaccinee.Sabin vaccine: Here the virus is alive but attentiated I.e. it can replicate but does not produce disese. It can still induce an immune response. This is the most widelty used vaccine particurlt in the UK. It produces the most efficient immune response.Influenza A virus is the second acute infection to be discussed.MyxovirusEnveloped virus with a segmented RNA genomeInfects a wide range of animals other than humansUndergoes extensive antigenic variationMajor cause of respiratory infectionsRespiratory aerosoles can be generated from the respiratory tract by various means from speaking to sneezing.

During a sneeze, millions of tiny droplets of water and mucus are expelled at about 200 miles per hour (100 metres per second). The droplets initially are about 10-100 micrometres diameter, but they dry rapidly to droplet nuclei of 1-4 micrometres, containing virus particles or bacteria. This is a major means of transmission of several diseases of humans.

There are various means by which the host is protected from infection by influenza virus.The droplets containg the virus may be filtered by fines hairs and cilia in the nasal cavity.Muco-cilliary cells lining the trachea can trap virus particles and sweep the virus to the back of the throat from where it is swallowed and excreted via the intestinal tract.Alveolar macrophages can engulf the virus if it enteres as far as the lower reaches of the lung and alveolar sac.Epstein Barr VirusBurkitts LymphomaHuman papillomavirusBenign wartsCervical CarcinomaHuman T-cell Lymphoma Virus (HTLV-1)LekaemiaHepatitis C virusLiver carcinoma The following points should be noted for virus-induced tumours: Virus infects cell: The infection process of an uninfected cell by the virus follows the standard pathway. Virus nucleic acid, as DNA, integrates into cellular genome: In the majority of virus tumours the virus nucleic acid integrates and physically joins with the cellular genome DNA. This contrasts with the HSV latent infection where the virus nucleic acid remains independent from the cellular genome.For retroviruses, which have RNA as their genomic nucleic acid, a DNA copy of the virus genome RNA is made.The virus may remain integrated with the cell for an extended period without any overt sign of infection. Virus causes changes in cellular gene expression: Because the virus nucleic acid is physically incorporated into the cell genome it can influence gene expression either through the introduction of new genes (already present in the virus genome) or by activating cell genes in an uncontrolled manner.Uncontrolled cell multiplication and tumour formation: The end result of the altered gene expression is the deregulation of cell growth with the formation of a tumour.