virus - Birdi

CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
Why we have virology course?
• Causing a lot of serious diseases
• No medical treatment
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
What we have in General virology course?
Carter and Saunders
2007
Chapters 1-10
[email protected]
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Content of General virology course
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Chapter 1: Viruses and their important
Chapter 2: Methods used in virology
Chapter 3: Virus structure
Chapter 4: Virus transmission
Chapter 5: Attachment and entry of viruses into cells
Chapter 6: Transcription, Translation and Transport
Chapter 7: Virus Genome Replication
Chapter 8: Assembly and exit of virions from cells
Chapter 9: Classification and nomenclature of viruses
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
Assigments
MABI: Plant Virology Lectures
1. Papova- / papillomaviruses
(small ds DNA)
2. Herpesviruses (large ds DNA)
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Cervical cancer
Chicken pox
3. Picornaviruses (+ve ss RNA)
Polio
4. Orthomyxoviruses (-ve ss RNA)
Flu
5. Retroviruses (RNA/DNA)
HIV - AIDS
6. Hepadnavirus complex
Hepatitis Virus
7. Baculovirus (insect virus)
Biocontrol
8. Plant viruses
Agropathogen
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
Assigments
MABI: Plant Virology Lectures
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1. What (Structure)
2. Where? When? (History)
3. How - Who? (Epidemiology - transmission)
4. Transcription mechanism (related to structure - host)
5. Translation mechanism (related to structure - host)
6. Researches about this virus (method)
7. How to prevent – treat
8. Remain problems in research of this virus
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Chapter 1: Viruses and their important
Flu
1. Viruses are ubiquitous on Earth
2. Reasons for studying viruses
3. The beginning of virology
Bacteriophage
4. The nature of viruses (virus definition)
HIV
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Viruses are ubiquitous on Earth
1. Viruses infect all cellular forms:
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Eukaryotes (vertebrate/invertebrate animals; plants; fungi)
Prokaryotes (bacteria and archaea): bacteriophages
2. Presence of viruses
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3.
4.
Sign of diseases
Non-pathogenic virus infection
Integrated into host genomes
In soil, air and water (or aqueous environment)
Correlation between studied intensive of species ><number of found
viruses: human virus >>> E. coli
Only tiny fraction of viruses was discovered – new potential hosts –
non-cultivable bacteria
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Reasons for studying viruses
1. Some viruses are harmful:
–
Hepatitis C
–
HIV
Causing disease: trivial (common
colds) – cancer – affect well-being of
societies (smallpox-AIDS) - lethal
(rabies)
Causing the most economic impact:
viruses in Veterinary – plant – dairy
* Need :
– Understanding the (nature – replication
- ways of causing disease) of viruses
– Development of : prevention –
diagnosis – treatment (vaccines,
reagents, techniques, anti-viral drugs)
Smallpox
Bacteriophage
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Reasons for studying viruses
2. Some viruses are useful:
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Phage typing of bacteria : Salmonella (epidemiological
information)
Sources of enzymes: reverse transcriptase (retroviruses) – RNA
polymerases (phages)
Pesticides: baculoviruses (insect pests) – Myxoma viruses
(rabbits)
Anti-bacterial agents: >< antibiotic - resistant bacteria strains)
Anti-cancer agents: genetically modified of herpes simplex and
vaccinia viruses
Gene vectors for protein production: baculoviruses and
adenoviruses
Gene vectors for treatment of genetic diseases : retroviruses
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Reasons for studying viruses
3. Virus studies have contributed to knowledge: molecular biology - cell
biology – cancer
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Genes are composed of DNA: (Phage T2 and E.coli)
The first characterized enhancer: (Simian virus (SV40)
The first characterized transcription factor: (transplantation antigen of
SV40)
The first nuclear localization signal (NLS): (transplantation antigen of
SV40)
Introns: studies of Adenovirus transcription
Role of cap structure at 5‟ end of Ekaryote mRNA: vaccinia and
reovirus
The first internal ribosomal entry site (IRES): RNA of poliovirus
The first RNA pseudoknot : in genome of turnip yellow mosaic virus
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
The beginning of Virology
Adolf Mayer
(1843-1942)
Mayer ("Rijkslandbouwschool
te Wageningen)
Reports in 1892 results on a study of
a tobacco mosaic disease. Believes
it is caused by a bacterium of some
kind, but attempts to isolate a
bacterium fail
Iwanowski
(1864-1920)
Ivanowski
On 12th February 1892, Dmitri
Iwanowski, a Russian botanist,
presented a paper to the St.
Petersburg Academy of Science
showing that extracts from diseased
tobacco plants could transmit disease
to other plants after passage through
ceramic filters fine enough to retain the
smallest known bacteria. Unfortunately,
Iwanowski did not fully realize the
significance of these results.
Beijerinck
(1851-1931)
Beijerinck
A few years later, in 1898, Martinus
Beijerinick confirmed & extended
Iwanowski's results on tobacco
mosaic virus & was the first to develop
the modern idea of the virus, which he
referred to as contagium vivum luidum
('soluble living germ').
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
Viruses
Influenza pandemic 2009
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Viruses that changed the course of history
Pharaoh
Ramses V
(Egypt) had
smallpox; he
died 1157 B.C.
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Report on
Aztec pox
The disease (and also measles) was transferred to America by the
Spanish, when they conquered the New World in the early 1500.
3.5 million Aztecs died in the next 2 years.
In the cities of 18th century Europe, smallpox reached plague
proportions and was a feared scourge - highly infectious.
Five reigning European monarchs died from smallpox during the
18th century.
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Viruses that changed the course of history
Poxvirus
Poxvirus +
influenzavirus
Human Immunodeficiency
Virus
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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The „Spanish‟ flu 1918
40 million deaths (more than on all battle fields of World War I combined)
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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The „Mexican‟ flu 2009
18,000 deaths (4%)
(1918: 40 million deaths)
Why is it called „Spanish‟ flu ?
And „Mexican „flu‟ ?
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Some examples of viruses and disease control
Smallpox virus:
irradicated in the 70’s
due to vaccination programss
Poliovirus:
irradication ongoing (> 2020)
Measles: future
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Chicken pox and shingles (girdle herpes)
Rash versus neuralgia
caused by a
herpesvirus
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Human papillomavirus (HPV; “wart virus”)
Example of
a mostly
benign virus
Some variants however
cause (cervical) cancer
Starting 2009, a vaccine against
cervical cancer-causing HPV is part
of a national vaccination program.
(Netherlands, Europe)
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
HIV-infection can lead to AIDS
Acquired ImmunoDeficiency Syndrome: Virus targets the immune system
Breaks down the immune system:
opportunistic infections
such as by Candida lead to
100 % mortality
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Small causes, large consequences
an extremely infectious picornavirus (pico = small)
28 nm
Foot-and-Mouth Disease Virus (FMDV)
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
Herpes simplex virus (HSV)
example of an isometric
(spherical) virus
(envelope partially removed)
Cf. Olympic Equestry in Hongkong in 2008
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
Atomic model of a picornavirus
poliovirus, common cold virus, FMDV
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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New outbreaks of existing or newSeals
viruses
Infectious diseases often
dictate population dynamics
Phocine distemper
virus
(epizootic every decade or
so in the Dutch Wadden Sea)
Relative of measles and rubella
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Viruses of other organisms than vertebrates ?
Plants: potato, tomato, tobacco
Insects
Fungi
Bacteria
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Routes of virus transmission
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Air
Water
Contact
Food
Vectors
influenza, SARS
polio, diarrhea
HIV, Ebola, herpes
norovirus
West Nile virus,
Chikungunya, Hendra,
yellow fever
– Mosquitoes and ticks
• Vertical
plant virus
– Germ line
Bats: SARS, Hendra
= virus reservoir
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Some recent virus outbreaks
Virus
Way of transmission
HIV
blood
Ebola
blood
Classical swine fever
aerosol
Foot-and-mouth disease
aerosol
Human / Avian influenza
aerosol
SARS
aerosol
Norovirus
food
Dengue
mosquito
West Nile virus
mosquito
Bluetongue (sheep)
mosquito
Peppino mosaic virus (pepper)
contact
White spot syndrome virus (shrimp)
canibalism
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Examples of virus disease: Tulip breaking virus
Tulipomania
When first desribed it was assumed that the colour
beautification was an endevour of the tulips to please their
masters eyes before bidding a last farewell prior to
evanescence.
Potyvirus; 750 nm - Ø12 nm
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
The nature of viruses
Viruses are the smallest genetic entities
POLIOVIRUS
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Viral genome sizes compared to those of cellular organisms
human
6.000.000.000
mammals
yeast
10.600.000
Viruses:
• Submicroscopic
• DNA or RNA
• need cells to replicate
• intracellular parasites
plants
E. coli
4.700.000
fungi
MS2
3.500
CMV
230.000
bacteria
viruses
102
103
104
105
106
107
108
Genome sizes (basepairs)
109
1010
1011
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
A virus is an encapsidated piece of genetic information (RNA or DNA) which replicates
on the expense of the host (cell), thus causing an (infectious) disease
Protecting protein coat
RNA or DNA genome
Penetration
of cell
Host cell
replication
Nucleus
progeny virus
103-106 per cell
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
The nature of viruses
• Viruses are smallest genetic entity
• Viruses have genes :
• RNA or DNA / single or double stranded
• nucleic acid + protein(s) (+ lipid membrane)
• Viruses lack many prerequisites for “life”
• no enzymes for metabolism
• no ribosomes -- absence of de novo protein synthesis
• Manifestation only in living host
• Use host cell proteins
• Code efficiently
• Many virus proteins are multifunctional
• Obligate parasites
• Capable of surviving outside the host
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Composition of viruses
1. Nucleic acid
2. Protein
3. Lipids
RNA [>90% of all plant viruses]
DNA [<10%]
coat or capsid protein,
glycoproteins
surrounding membrane or
envelop
ds or ss
one or more segments
2 - 15 genes
Coat protein:
protection of genetic material
recognition of host (plant)
crucial in virus transmission
(virus-vector interactions)
only some viruses
obtained from host cell
always contains glycoproteins
(GP)
20 - 200 nm
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Virus definition
Virus is a very small, non-cellular
parasite of cell. Its genome, which is
composed of either DNA or RNA, is
enclosed in a protein coat.
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Are viruses living or nonliving?
“ Viruses belong to biology because they possess
genes, replicate, evolve and are adapted to particular
hosts / biotic habitats / ecological niches.
However, ….they are non living infectious entities that
can be said, at best, to lead a kind of borrowed life”
Marc van Regenmortel and Brian Mahy (2004)
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Diversity of viruses
Virosphere
Bacteria
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Diversity of viruses
Virosphere
Bacteria
Laboratory of Virology
Families and Genera
of Plant viruses
MABI: Plant Virology Lectures
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Laboratory of Virology
MABI: Plant Virology Lectures
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Classification of
animal-infecting
viruses
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Classification of (plant)viruses
(-DNA)
+DNA (55)
Pseudoviridae
+RNA
VI
-DNA
e.g. Geminiviruses
II
+/-DNA (37)
I
III
+RNA (699)
Most plant viruses
-RNA
IV
+mRNA
+/-RNA (47)
e.g. Reoviruses
V
-RNA (71)
Total no. plant viruses = 909
e.g. Tospoviruses
Baltimore (1971)
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
Basic form of viruses
• Viruses are
– Isosahedral
– Helical
– Complex
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
Morphology of virus particles
Capsid proteins are arranged
in a sphere following the basic
shape of the icosahedron or
triangulated forms of it.
Capsid proteins are arranged
helically to form a rod-shapes
coat protecting the nucleic
acid
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CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
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Morphology of plant viruses
CPMV
MSV
TMV
PVY
• Isometric viruses (spherical)
• Rod-shaped viruses
TSWV
• Complex viruses
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
CANTHO UNIVERSITY
Laboratory
of Virology
BiRDI
MABI: Plant Virology Lectures
WAGENINGEN UR
Learning outcomes
1. Discuss reasons for studying viruses
2. Explain how viruses differ from other organisms
3. Define the term “virus”