This document provides an introduction to viruses, covering their structure, replication, infections they cause, and treatments. It discusses that viruses are submicroscopic entities that can only replicate within host cells. Their structure includes a protein coat that surrounds genetic material. Viruses infect and destroy host cells, and different viruses cause infections through various transmission routes like respiratory or sexual contact. Treatments include antiviral drugs that target specific virus life cycle stages, as well as vaccines that stimulate protective immunity.
2. Lecture topics - 1
•
What is a virus?
Definition
Structure and replication
•
•
Human virus infections
Treatment
Antivirals
Vaccines
3. Lecture topics – 2
•
Immunity to viruses
Cell-mediated
Humoral
•
•
Role of Complement
Vaccination against viruses
Inactivated vaccines
Live vaccines
•
Interferon
4. Definition of a Virus
Sub microscopic entity consisting
of a single nucleic acid surrounded
by a protein coat and capable of
replication only within the living
cells of bacteria, animals or
plants.
11. Transmission of Viruses
•
•
•
•
•
Respiratory transmission
Influenza A virus
Faecal-oral transmission
Enterovirus
Blood-borne transmission
Hepatitis B virus
Sexual Transmission
HIV
Animal or insect vectors
Rabies virus
12. Virus Tissue Tropism
•
Targeting of the virus to specific tissue
and cell types
•
Receptor Recognition
CD4+ cells infected by HIV
CD155 acts as the receptor for
poliovirus
13. In vivo Disease Processes
•
Cell destruction
•
Virus-induced changes to gene
expression
•
Immunopathogenic disease
17. Poliovirus
Properties of the virus
•
•
•
•
Enterovirus.
Possesses a RNA
genome.
Transmitted by the
faecal oral route.
Cause of
gastrointestinal illness
and poliomyelitis.
19. Incidence of Poliomyelitis
Number of cases (in thousands)
A
B
40
Poliovirus vaccines
A: Salk – killed inactivated
vaccine.
B: Sabin – live attenuated
vaccine
30
20
10
0
1950
1960
1970
1980
20. Influenza A virus
Properties of the virus
•
•
•
•
•
Myxovirus
Enveloped virus with a
segmented RNA
genome
Infects a wide range of
animals other than
humans
Undergoes extensive
antigenic variation
Major cause of
respiratory infections
21. Influenza A virus Infection
•
•
•
Spread by respiratory route
Virus infects cells of the respiratory
tract
Destruction of respiratory epithelium
Secondary bacterial infections
•
Altered cytokine expression leading to
fever
e.g interleukin-1 and interferon
24. Weekly consultation rates for influenza and influenza-like illness: Weekly
Returns Service of the Royal College of General Practitioners, 1988 to
1999
Rate per 100 000 population
600
500
Epidemic activity
400
300
200
Higher than expected
seasonal activity
Baseline activity
Normal seasonal activity
100
0
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999
Year
CDR Weekly Report: 5th November 1999
25. Generation of Novel Influenza A Viruses
Human H2N2
ANTIGENIC SHIFT
Genetic Reassortment
Avian H3N8
Point mutation of HA and NA
genes
ANTIGENIC DRIFT
Human H3N2
26. Viruses and Human Tumours
•
Epstein Barr Virus
Burkitt’s Lymphoma
•
Human papillomavirus
Benign warts
Cervical Carcinoma
•
Human T-cell Leukaemia Virus (HTLV-1)
Leukaemia
•
Hepatitis C virus
Liver carcinoma
These two lectures will review some features of viruses from the basic virology to the development of immunity to virus infections.
Lecture 1
Primarily concerned with the basic details of virus replication and pathogenesis.
Lecture 2
Development of the immune response
What is a virus
“Sub microscopic entities consisting of a single nucleic acid surrounded by a protein coat and capable of replication only within the living cells of bacteria, animals or plants.”[1]
The key features of this definition are as follows:
Single type of nucleic acid – either DNA or RNA but not both
Replication of the virus only with a living cell – they are obligate intracellular parasites.
These characteristics are typical for ALL viruses whether they infect bacteria, plants or animals. [1] Adapted from Collins English Dictionary
What is a virus
“Sub microscopic entities consisting of a single nucleic acid surrounded by a protein coat and capable of replication only within the living cells of bacteria, animals or plants.”[1]
The key features of this definition are as follows:
Single type of nucleic acid – either DNA or RNA but not both
Replication of the virus only with a living cell – they are obligate intracellular parasites.
These characteristics are typical for ALL viruses whether they infect bacteria, plants or animals. [1] Adapted from Collins English Dictionary
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This overhead shows the standard features found in some (but not all) viruses.
A virus particle is essentially a piece of nucleic acid surrounded by a protein coat.
The protein coat (i.e. the capsid) is a delivery system for transferring the virus genome from one cell to another. The protein serves to:
Provide protection to the nucleic acid against the environment - e.g. nucleases etc.
Function in receptor recognition - targeting a virus to a susceptible host and cell type.
Surrounding this coat there may be a lipid envelope - this envelope is derived from one of the cell membranes and is not determined by the virus. There may be some modification to the lipid composition induced during virus maturation.
Inserted into the lipid envelope there are usually virus proteins which are present as spike projections - these are normally glycoproteins.
Due to restrictions on the coding size of many virus genomes the capsid of the virion is made up of repeating subunits, which coat the virus genomic nucleic acid. The redundancy also allows for the fact that if there is an inactivation of part of the capsid the virus does not completely lose its infectivity For example the poliovirus RNA (7kb) can specific at most 250,000 Daltons of protein altogether (some must be used for replication) but the poliovirus virion capsid weighs 6 x 106 Daltons.
Genomic Nucleic Acid
Viruses only possess a single type of genomic nucleic acid – either DNA or RNA but not both. This nucleic acid can be in a variety of physicla forms that can be used as a valuable classification feature.
The virions that you will see have the following common features:
Simple structure
The overall structure is not in general complex although they do perform complex functions (protection of the genome and entry of the virus to the cell)
Repeating structure
They are generally made up a very few proteins (the simple plant viruses may just have one protein in the virus capsid) OR proteins which are structurally very similar.
High Level of Redundancy
There is a high degree of redundancy in the virion, which allows for the partial inactivation of some parts of the virion without actually destroying the virion completely. The general exceptions to these comments are the poxviruses.
1.1. Virion Types
The majority of viruses fall within one of two basic structures:
Helical virions
Icosahedral virions
The features of each of these are described in the following.
1.1.1. Helical Virions
Common form of structure in which the capsomeres wrap around the nucleic acid to produce a helix. In plant viruses this helix may be “naked” whereas in the case of viruses infecting animals all viruses have an envelope surrounding the capsid structure.
The diameter of the helical capsid is determined by the characteristics of the capsomeres and the length of the nucleic acid molecule determines the length of the helix.
1.1.2. Icosahedral Virions
The only closed shell that can be made with repeating capsomeres is an icosahedron. The simplest icosahedron is a regular solid with 12 vertices and 20 triangular faces - to make this shell there must be sixty identical protomers (i.e. 3 per face)[2].
Larger viruses have a more complex virion. Each triangular face of the icosahedron is divided into six half-triangles. The corners of the inscribed faces are solid lines; those of the basic faces are dashed lines. Monomers are arranged in pentons around the fivefold axis and in hexons around the threefold axis. In the case of poliovirus each of the sixty subunits is made up of three monomers VP1, VP2 and VP3.
In higher order capsids still the proteins located at the pentons and hexons are distinct proteins - for example in adenovirus the hexons contain three protomers rather than six as in the basic icosahedron.
Icosahedral particles may exist as either naked or enveloped virions.
[1] Naked viruses with helical virions (e.g. plant viruses) are more tightly packed.
[2] The smallest and simplest virions made up of 60 identical subunits are that of satellite tobacco mosaic virus. Possess a short RNA (~1600 bases) with just one gene that encoding the capsid protein. This virus can only replicate in cells already infected by tobacco necrosis virus. This virus is referred to as a satellite virus.
1.1.1. Complex virions
Not all viruses fall within these two simple categories and two examples will be given of so-called complex virions.
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There are many variations on the virus replication and this diagram illustrates some of the basic features of the cycle.
1. Attachment and entry: viruses recognise specific structures on the cell surface (referred to as virus receptors), which target the virus to specific cell types and tissue. This is one of the primary determinants for which tissues are infected by a particular virus. The receptor is a normal component of the cell, which the virus has hijacked for the infection process.
2. Uncoating: The virion breaks open and releases the virus genome nucleic acid into the host cell cytoplasm. Further replication may take place in the cytoplasm or the nucleic acid may migrate to the cell’s nucleus.
3. Transcription: Virus mRNA is produced using either cellular enzymes or virus-coded enzymes.
4. Genome replication: This stage can take place in either the cytoplasm or nucleus of the infected cell. Depending on the size of the virus genome the enzymes involved in genome replication may be encoded by either the virus itself or the host cell.
5. Translation: This stage uses the host cell machinery - ribosomes and enzymes etc. Various proteins are synthesised - structural - only in virion - and non-structural - detected only in the virus-infected cell.
6. Virion Assembly: The newly formed virus proteins and genomic nucleic acid assemble to produce the new virus particles.
7. Virion release: Various strategies are available for the release of the progeny virus from the infected cell depending on the particular virus group. The virus may bud through the cell membrane at which time it picks up the envelope surrounding the virus particle OR the virus may simply cause lysis of the cell resulting in cell death and the release of progeny virus particles.
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Cell death – Cytopathic effect
This is the end result of many lytic virus infections in which the cell is killed following virus infection. This end result of virus infection is the cause of cpe found in cell culture systems infected with lytic viruses. The form of virus-induced cpe can take many forms ranging from the lysis of the cell to a fusion event with the formation of syncytia.
Persistent infection
The outcome of some virus infections is not cell death but the development of a persistent (or chronic) virus infection. This differs from the transformation of cells (described below) since in many cases the cells appear similar (or identical) to the uninfected parental cell line. The cells may continue to grow in culture and release infectious virus.
These infections are characterised by the virus normally being lytic but under specific situations (e.g. host cell type) the virus establishes a chronic or persistent infection.
Latent Infection
The capacity of herpes virus to establish a latent infection is essentially another form of persistent infection. In this case the virus is not actually replicating but lying dormant in the host cell
Transformation
A transformed cell in vitro or a tumour developing in vivo is essentially a cell-type, which shows no control over its cell division with unregulated growth.
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.
An Importatnt statge in virus pathogenesis is the targetting of the virus for a specific tissue or cell type. This is achieved at the initial stage of virus replication when the virus recognises a receptor on the cell surface.
There are various receptors defined for viruses and two are shown here:
CD4+ cells are infected with HIV – these are largely T4 helper cells
CD155 is the receptor for poliovirus and the pattern of the expression of this protein folows the specifi cells infected by poliovirus under natural conditions.
The diseases caused by viruses are due to a number of mechanisms of which the major ones are as follows (these have analogies to the manner in which the virus interacts with cells in vitro):
Cell destruction following virus infection: Essentially the virus infection leads to the death of the infected cells. This is equivalent to the cytopathic effect observed during the infection of cells in vitro.
Virus-induced changes to cellular gene expression: The presence of the virus within the host cell may lead to virus-induced changes in the expression of specific cellular genes. This will be discussed further with respect to the occurrence of virus-induced tumours.
Immunopathogenic disease: Some viruses may induce changes in the pattern of the immune response by the host - e.g. infection of specific cells in the immune system, altered exposure of host antigens to the immune system, disturbed expression of specific cytokines during virus infection.
The graph illustrates the typical pattern of virus replication during an acute virus infection:
Following a short incubation period of a few days there a maximal virus production
Visible symptoms generally appear just after this peak of virus replication. Depending on the virus the symptoms may last just a few days.
The patient recovers and an immune response is generated and the virus is eliminated within 1 or 2 weeks.
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.
A human virus infection that is largely controlled by vaccination and is likely to be fully eradicated in the next few years.
The infection here is associated with infantile paralysis affecting the lower limbs but in severe cases there can be paralysis of the muscles controlling respiration.
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.
Myxovirus
Enveloped virus with a segmented RNA genome
Infects a wide range of animals other than humans
Undergoes extensive antigenic variation
Major cause of respiratory infections
Respiratory 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.
Virus epidemiology
Infleunza A virus shows regular outbreaks during the winger months.
These are either
Eopidenics: widespread outbreaks within the coutry
Pandemics: Worldwide outbreaks of the virus affecting large numbers of people.
Epstein Barr Virus
Burkitt’s Lymphoma
Human papillomavirus
Benign warts
Cervical Carcinoma
Human T-cell Lymphoma Virus (HTLV-1)
Lekaemia
Hepatitis C virus
Liver carcinoma
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Virus trasnformed cells show a complete deregulation of their normal growth. They tend to pile up over each other and do not stop growing as is typical of normal uninfected/non-trasnformed cells.
This change in the phenotype is due to the virus influencing the gene reulation of the cell. Many of the cellular genes affected that lead to the trasnformed pheotype are associated with gowth regulation and signal recognittion.
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.
Antivirals
Vaccines and immunisation
Attachment/Entry
Picornaviruses
Nucleic acid replication
Human immunoideficiency virus (AZT)
Herpes simplex virus (Acyclovir)
Virus protein processing
HIV (Protease inhbitors)
Virus maturation
Influenza A virus (Neuraminidase blockers)
Problems of antivruals
Dificuly in finding a virus specific site against which to direct the antivrial
As with the use of antiiotics – resistant mutant scan be readily generated that are resistant to antiirals – this is particuarly a problem with those against HIV where the drug has to be used for prolonged periods of time.