Basics of Virology.ppt...................

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1. Dinda Victor
Masinde Muliro University Science and
Technology
BMB 416
Review Basics of Virology
INTRODUCTIONS TO
VIROLOGY

2. General Introduction
Virologyis the study of viruses
submicroscopic, parasitic particles of genetic
material contained in a protein coat and virus-like
agents.
It focuses on the following aspects of viruses:
heir structure, classification and evolution, their
ways to infect and exploit host cells for
reproduction, their interaction with host organism
physiology and immunity
the diseases they cause, the techniques to isolate
and culture them, and their use in research and
therapy.
Virology is considered to be a subfield of
microbiology or of medicine

3. General Introduction
Mycologyis the branch of biology concerned with the
study of fungi,
including their genetic and biochemical properties,
their taxonomy and their use to humans as a source
for medicine (e.g., penicillin), food (e.g., beer, wine,
cheese, edible mushrooms), as well as their dangers,
such as poisoning or infection.
A biologist specializing in mycology is called a
mycologist.
From mycology arose the field of phytopathology, the
study of plant diseases, and the two disciplines
remain closely related because the vast majority of
"plant" pathogens are fungi.

4. Origin of Virological
Knowledge
The Origins of Virology Ancient peoples were not only
aware of the effects of virus infection, but in some
instances also carried out research into the causes &
prevention of virus diseases.
Perhaps the first written record of a virus infection
consists of a heiroglyph from Memphis, the capital of
ancient Egypt, drawn in approximately 3700BC, which
depicts a temple priest called Ruma showing typical
clinical signs of paralytic poliomyelitis.
The Pharaoh Siptah ruled Egypt from 1200-1193 BC
when he died suddenly at the age of about 20.

5. Origin of Virological
Knowledge
His mummified body laid undisturbed in his tomb in
the Valley of the Kings until 1905 when the tomb was
excavated.
The mummy shows that his left leg was withered and
his foot was rigidly extended like a horse's hoof -
classic paralytic poliomyelitis
In addition, the Pharoh Ramses V, who died in
1196BC, is believed to have succumbed to smallpox
-compare the pustular lesions on the face of the
mummy & those of more recent patients.

6. Origin of Virological
Knowledge
Smallpox was endemic in China by 1000BC.
In response, the practice of variolation was
developed.
Recognizing that survivors of smallpox outbreaks
were protected from subsequent infection,
variolation involved inhalation of the dried crusts
from smallpox lesions like snuff, or in later
modifications, inoculation of the pus from a lesion
into a scratch on the forearm of a child.
Lady Mary Wortley Montagu introduced
Variolation to England

7. Origin of Virological
Knowledge
On 14th May 1796, Edward Jenner used cowpox-
infected material obtained from the hand of Sarah
Nemes, a milkmaid from his home village of Berkley
in Gloucestershire to successfully vaccinate 8 year
old James Phipps.
On 1st July 1796, Jenner challenged the boy by
deliberately inoculating him with material from a real
case of smallpox !
He did not become infected
Although initially controversial, vaccination against
smallpox was almost universally adopted worldwide
during the 19th century

8. Origin of Virological
Knowledge
Rabies was one of the Most Feared Diseases of
Man Mesopotanian laws concerning rabid dogs
date from 1000 BC.
People who let rabid dogs run free were fined.
Rabies is known on all continents.
Recent epidemics in North America, Europe &
India. Rabies virus causes disease and death in
most mammals.
Transmitted in nature by foxes, raccoons, skunks
and bats to domestic animals. Dogs and bats
transmit to humans

9. Origin of Virological
Knowledge
Robert Koch (1843-1910) However, it was not until
Robert Koch & Louis Pasteur jointly proposed the
'germ theory' of disease in the 1880s that the
significance of these organisms became apparent.
Koch defined the four famous criteria now known as
Koch's postulates which are still generally regarded
as the proof that an infectious agent is responsible
for a specific disease.
Subsequently, Pasteur worked extensively on rabies,
which he identified as being caused by a 'virus' (from
the Latin for 'poison')
but in spite of this, he did not discriminate between
bacterial & other agents of disease Louis pasteur.

10. Origin of Virological
Knowledge
Dmitri Iwanowski (1864-1920) On 12th February
1892, Dmitri Iwanowski, a Russian botanist,
presented a paper to the St. Petersburg Academy
of Science which showed 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.
This is generally recognised as the beginning of
Virology.
Unfortunately, Iwanowski did not fully realize the
significance of these results.

11. Origin of Virological
Knowledge
Martinus Beijerinick (1851-1931) Found that the
agent could reproduce only in the host and was
not inactivated by alcohol.
Called the agent a “contagium vivum fluidum” or a
“contageous living liquid”.
Clearly stated that the agent was not a bacterium,
fungus or other culturable pathogen.
He is known as the “Father of Virology

12. Origin of Virological
Knowledge
FreidrichLoeffler(1852-1915) Proof that Animal
Diseases can be Caused by Viruses F.A.J. Loeffler
(left) and P. Froschworking in 1898 with Robert
Kosch(right) in Germany discovered the first
vertebrate virus, foot-and-mouth disease virus, with
filters that held back bacteria.
Walter Reed (1900) showed that yellow fever in
humans was caused by a filterable virus that was
transmitted by mosquitoes
Ellermanand Bang (1908) demonstrated that
leukemiain chickens was caused by a virus
Peyton Rous (1911) showed that muscle tumorsin
chickens were caused by a virus that later was shown
to be a retrovirus.
Won Nobel Prize in 1962 at age 84

13. Origin of Virological Knowledge
Frederick Twort (in 1915) & Felix d'Herelle (in 1917)
were the first to recognize viruses which infect
bacteria, which d'Herelle called bacteriophages
(eaters of bacteria).
In the 1930s & subsequent decades, pioneering
virologists such as Luria, Delbruck & many others
utilized these viruses as model systems to
investigate many aspects of virology , including virus
structure, genetics, replication, etc.

14. Origin of Virological
Knowledge
TMV was crystallized in 1935 by Wendell Stanley
and shown to be largely protein.
Stanley demonstrated that viruses can be
analyzed according the laws of chemistry, as well
as biology.
However, Bawden & Pirie Crystallized tomato
bushy stunt virus and TMV in 1936 and found that
they contained phosphorous and concluded that
the viruses were nucleoproteins.

15. Origin of Virological Knowledge
This finding set the stage for nucleic acid analyses.
Wendell Stanley Virus Crystal
In the 1940’s Development of Electron Microscopy
revealed that viruses have different shapes.
TMV and many other viruses are rod-shaped. Other
viruses such as tomato bushy stunt virus are
spherical.
Early EM of TMV 1956-Crick and Watson propose
that virus particles consist of many identical protein
subunits.

16. Nature of the Virus
There are 6 basic characteristics of a virion
Namely
Size.
The size range of viruses is from about 20 to 300 nm.
viruses are much smaller than bacteria. Most animal
viruses and all plant viruses and phages
are invisible under the light microscope.
submicroscopic

17. Nature of the Virus
Simple structure.
Viruses have very simple structures.
The simplest viruses are nucleoprotein particles
consisting of genetic material (DNA or RNA)
surrounded by a protein capsid.
The more complex viruses contain lipids and
carbohydrates in addition to proteins and nucleic acids, e.
g. the enveloped viruses

18. Nature of the Virus
Absence of cellular structure.
Viruses do not have any cytoplasm, and
thus cytoplasmic organelles like mitochondria, Golgi
complexes, lysosomes, ribosomes, etc., are absent.
They do not have any limiting cell membrane.
They utilize the ribosomes of the host cell for protein
synthesis during reproduction.

19. Nature of the Virus
No independent metabolism.
Viruses cannot multiply outside a living cell.
No virus has been cultivated in a cell-free medium.
Viruses do not have an independent metabolism.
They are metabolically inactive outside the host cell
because they do not posses enzyme systems and protein
synthesis machinery
Viral nucleic acid replicates by utilizing the protein synthesis
machinery of the host.
It codes for the synthesis of a limited number of viral proteins,
including the subunits or capsomeresof the capsid,
the tail protein and some enzymes concerned Viruses have
only one nucleic acid, either DNA or RNA.

20. Nature of the Virus
Typical cells have both DNA and RNA.
Genomes of certain with the synthesis or the
release of virions.
Nucleic acids.
RNA viruses can be transcribed into complementary DNA
strands in
the infected host cells, e. g. Rous Sarcoma Virus (RSV).
Such RNA viruses are therefore also called RNA-DNA
viruses.

21. Nature of the Virus
Crystallization.
Many of the smaller viruses can be crystallized, and thus
behave like chemicals.
No growth and division.
Viruses do not have the power of growth and division.
A fully formed virus does not increase in, size by
addition of new molecules. The virus itself cannot divide.


22. Nature of the Virus
Only its genetic material (RNA or DNA) is capable of
reproduction and that too only in a host cell.
It will thus be seen that viruses do not show all the
characteristics of typical living organisms.
•They, however, possess two fundamental characteristics
of living systems.
Firstly, they contain nucleic acid as their genetic material.
The nucleic acid contains instructions for the structure
and function of the virus.
Secondly, they can reproduce themselves, even if only
by using the host cells synthesis machinery.

23. Structure of the virus
Viruses display a wide diversity of shapes and sizes,
called morphologies.
Viruses are about 1/100th the size of bacteria.
Most viruses are unable to be seen with a light
microscope,
so scanning and transmission electron microscopes are
used to visualize virus particles.

24. Structure of the virus
A complete virus particle, known as a virion,
consists of nucleic acid surrounded by a protective coat
of protein called a capsid.
These are formed from identical protein subunits
called capsomers.
Viruses can have a lipid "envelope" derived from the
host cell membrane.

25. Structure of the virus
The capsid is made from proteins encoded by the viral
genome
and its shape serves as the basis for morphological
distinction.
Virally coded protein subunits will self-assemble to
form a capsid,
generally requiring the presence of the virus genome.

26. Structure of the virus
However, complex viruses code for proteins that assist
in the construction of their capsid.
Proteins associated with nucleic acid are known as
nucleoproteins,
and the association of viral capsid proteins with viral
nucleic acid is called a nucleocapsid.

27. Viral Morphologies
In general, there are four main morphological virus types.
Helical
These viruses are composed of a single type of
capsomeres
stacked around a central axis to form a helical structure,
which may have a central cavity, or hollow tube.

28. HelicalMorphology
This arrangement results in rod-shaped or filamentous
virions:
these can be short and highly rigid, or long and very
flexible.
The genetic material, generally single-stranded RNA,
but ssDNA in some cases, is bound into the protein
helix,

29. HelicalMorphology
by interactions between the negatively charged nucleic
acid and
positive charges on the protein.
the length of a helical capsid is related to the length of the
nucleic acid contained within it and the diameter is
dependent on the size and arrangement of capsomeres.
The well-studied Tobacco mosaic virus is an example of a
helical virus.

30. HelicalMorphology

31. IcosahedralMorphology
Most animal viruses are icosahedral or
near-spherical with icosahedral symmetry.
A regular icosahedron is the optimum way of
forming a closed shell from identical sub-units.
The minimum number of identical capsomeres
required is twelve,

32. IcosahedralMorphology
each composed of five identical sub-units.
Many viruses, such as rotavirus, have more than
twelve capsomers
and appear spherical but they retain this
symmetry.
Capsomers at the apices are surrounded by five
other capsomers

33. IcosahedralMorphology
and are called pentons.
Capsomers on the triangular faces are surround
by six others and are call hexons

34. Envelope
Some species of virus envelope themselves in a
modified form of one of the cell membranes,
either the outer membrane surrounding an
infected host cell,
or internal membranes such as nuclear
membrane or endoplasmic reticulum,
thus gaining an outer lipid bilayer known as a viral
envelope.

35. Envelope
This membrane is studded with proteins coded for
by the viral genome
and host genome; the lipid membrane itself and
any carbohydrates
present originate entirely from the host.
The influenza virus and HIV use this strategy.
Most enveloped viruses are dependent on the
envelope for their infectivity.

36. Complex
These viruses possess a capsid that is neither purely
helical,
nor purely icosahedral, and that may possess extra
structures
such as protein tails or a complex outer wall.
Some bacteriophages, such as Enterobacteria phage T4

37. Complex
have a complex structure consisting of an icosahedral
head
bound to a helical tail, which may have a hexagonal
base plate
with protruding protein tail fibres.
This tail structure acts like a molecular syringe,
attaching to the bacterial host and
then injecting the viral genome into the cell.

38. The Viral Genome
An enormous variety of genomic structures can be
seen among viral species;
as a group they contain more structural genomic
diversity
than plants, animals, archaea, or bacteria.
Viruses have either DNA or RNA genes
and are called DNA viruses and RNA viruses
respectively.

39. The Viral Genome
Viral genomes are circular, such as polyomaviruses,
or linear, such as adenoviruses.
The type of nucleic acid is irrelevant to the shape of
the genome.
Among RNA viruses, the genome is often divided up
into separate parts
within the virion and is called segmented.

40. The Viral Genome
Each segment often codes for one protein and
they are usually found together in one capsid.
Every segment is not required to be in the same virion
for the overall virus to be infectious.
A viral genome, irrespective of nucleic acid type,
is either single-stranded or double-stranded.

41. The Viral Genome
Single-stranded genomes consist of an unpaired
nucleic acid,
analogous to one-half of a ladder split down the
middle.
Double-stranded genomes consist of two
complementary paired nucleic acids, analogous to a
ladder.

42. The Viral Genome
Some viruses, such as those belonging to the
Hepadnaviridae,
contain a genome that is partially double-stranded and
partially single-stranded.
For viruses with RNA or single-stranded DNA,
the strands are said to be either positive-sense (called
the plus-strand)

43. The Viral Genome
or negative-sense (called the minus-strand),
depending on whether it is complementary to the viral
messenger RNA (mRNA).
Positive-sense viral RNA is identical to viral mRNA
and thus can be immediately translated by the host cell.
Negative-sense viral RNA is complementary to mRNA

44. The Viral Genome
and thus must be converted to positive-sense RNA
by an RNA polymerase before translation.
DNA nomenclature is similar to RNA nomenclature,
in that the coding strandfor the viral mRNA is
complementary to it (−),
and the non-coding strandis a copy of it (+).

45. The Viral Genome
Genome size varies greatly between species.
The smallest viral genomes code for only four proteins
and
have a mass of about 10
6
Daltons;
the largest have a mass of about 10
8
Daltons and code
for over one hundred proteins.
RNA viruses generally have smaller genome sizes

46. The Viral Genome
than DNA viruses due to a higher error-rate when
replicating,
and have a maximum upper size limit.
Beyond this limit, errors in the genome when
replicating render the virus useless or uncompetitive.
To compensate for this, RNA viruses often have
segmented genomes where

47. The Viral Genome
the genome is split into smaller molecules, thus
reducing the chance of error.
In contrast, DNA viruses generally have larger
genomes
due to the high fidelity of their replication enzymes.

48. Taxonomy of Viruses
Classification/taxonomy seeks to describe the
diversity of viruses by naming and grouping them
based on similarities.
In 1962, André Lwoff, Robert Horne, and Paul
Tournier
were the first to develop a means of virus
classification,
based on the Linnaean hierarchical system

49. Taxonomy of Viruses
This system bases classification on phylum, class,
order, family, genus, and species.
Viruses were grouped according to their shared
properties (not of their hosts)
and the type of nucleic acid forming their genomes.
Later the International Committee on Taxonomy of
Viruses was formed.

50. Taxonomy of Viruses
There are two ways of classification of the viruses
The two classification systems borrows from different
schools of thoughts
The two classification systems include
ICTV classification
Baltimore Classification

51. ICTV classification
The International Committee on Taxonomy of Viruses
(ICTV)
developed the current classification system and
wrote guidelines that put a greater weight on
certain virus properties to maintain family uniformity.

52. ICTV classification
A universal system for classifying viruses, and a unified
taxonomy,
has been established since 1966.
The 7th lCTV Report formalized for the first time the
concept of the virus species
as the lowest taxon (group) in a branching hierarchy of
viral taxa.
However, at present only a small part of the total diversity
of viruses has been studied,

53. ICTV classification
with analyses of samples from humans finding that
about 20% of the virus
sequences recovered have not been seen before,
and samples from the environment, such as from
seawater and ocean sediments,
finding that the large majority of sequences are
completely novel.

54. ICTV classification
The general taxonomic structure is as follows:
Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species (-virus)

55. ICTV classification
In the current (2008) ICTV taxonomy, five orders have
been established, the
Caudovirales,
Herpesvirales,
Mononegavirales,
Nidovirales, and
Picornavirales.

56. ICTV classification
•The committee does not formally distinguish between
subspecies, strains, and isolates.
•In total there are 5 orders,
•82 families,
•11 subfamilies,
•307 genera,
•2,083 species and
•about 3,000 types yet unclassified.

57. Baltimore classification
The Baltimore Classification of viruses is based on the
method of viral mRNA synthesis.
Biologist David Baltimore devised the Baltimore
classification system.
The ICTV classification system is used in conjunction
with
the Baltimore classification system in modern virus
classification.

58. Baltimore classification
The Baltimore classification of viruses is based on the
mechanism of mRNA production.
Viruses must generate mRNAs from their genomes
to produce proteins and replicate themselves,
but different mechanisms are used to achieve this in
each virus family. :

59. Baltimore classification
Viral genomes may be single-stranded (ss) or double-
stranded (ds),
RNA or DNA, and may or may not use reverse
transcriptase (RT).
Additionally, ssRNA viruses may be either sense (+) or
antisense (-).
This classification places viruses into seven groups

60. Baltimore classification
I: dsDNA viruses(e.g. Adenoviruses, Herpesviruses,
Poxviruses)
II: ssDNA viruses(+)sense DNA (e.g. Parvoviruses)
III: dsRNA viruses(e.g. Reoviruses)
IV: (+)ssRNA viruses(+)sense RNA (e.g.
Picornaviruses, Togaviruses)

61. Baltimore classification
V: (-)ssRNA viruses(-)sense RNA (e.g.
Orthomyxoviruses, Rhabdoviruses)
VI: ssRNA-RT viruses(+)sense RNA with DNA
intermediate in life-cycle (e.g. Retroviruses)
VII: dsDNA-RT viruses(e.g. Hepadnaviruses)

62. Baltimore classification
As an example of viral classification,
the chicken pox virus, varicella zoster (VZV), belongs to
the order Herpesvirales,
family Herpesviridae,
subfamily Alphaherpesvirinae,
and genus Varicellovirus.
VZV is in Group I of the Baltimore Classification
because it is a dsDNA virus that does not use reverse
transcriptase.

63. Replication cycle of A Virus
Viral populations do not grow through cell division,
because they are a cellular; instead,
they use the machinery and metabolism of a host cell
to produce multiple copies of themselves, and they
assemblein the cell.
The life cycle of viruses differs greatly between
species
but there are six basicstages in the life cycle of
viruses:

64. Replication cycle of A Virus
Attachment
is a specific binding between viral capsid proteins
and specific receptors on the host cellular surface.
This specificity determines the host range of a virus.
For example, HIV infects only human T cells, because
its surface protein, gp120, can interact with CD4 and
receptors on the T cell's surface.
This mechanism has evolved to favourthose viruses that
only infect cells in which they are capable of replication.

65. Replication cycle of A Virus
Attachment to the receptor can induce the
viral-envelope protein to undergo changes
that results in the fusion of viral and cellular
membranes.
Penetration
follows attachment; viruses enter the host cell through
receptor mediated endocytosis or membrane fusion.
This is often called viral entry.
The infection of plant cells is different to that of
animal cells.

66. Replication cycle of A Virus
Plants have a rigid cell wall made of cellulose and
viruses can only get inside the cells following trauma
to the cell wall.
Viruses such as tobacco mosaic virus can also move
directly in plants,
from cell-to-cell, through pores called plasmodesmata.
Bacteria, like plants, have strong cell walls that a virus
must breach to infect the cell.
Some viruses have evolved mechanisms that
inject their genome into the bacterial cell while the
viral capsidremains outside

67. Replication cycle of A Virus
Uncoating
is a process in which the viral capsid is
degraded by viral enzymes or host enzymes
thus releasing the viral genomic nucleic acid.
Replication
involves synthesis of viral messenger RNA (mRNA)
for viruses
except positive sense RNA viruses,
viral protein synthesis and assembly of viral proteins
and viral genome replication.

68. Replication cycle of A Virus
Assembly
Following the assemblyof the virus particles,
post-translational modification of the viral proteins
often occurs.
In viruses such as HIV, this modification,
(sometimes called maturation), occurs afterthe virus
has been released from the host cell.

69. Replication cycle of A Virus
Release
Viruses are releasedfrom the host cell by lysis
a process that kills the cell by bursting its membrane.
Enveloped viruses (e.g., HIV) typically are released
from the host cell by budding.
During this process the virus acquires its envelope,
which is a modified piece of the host's plasma
membrane.
The genetic material within viruses, and the method by
which the material is replicated, vary between different
types of viruses.

70. Replication cycle of A Virus
DNA viruses
The genome replication of most DNA viruses takes
place in the cell's nucleus.
If the cell has the appropriate receptor on its surface,
these viruses enter the cell by fusion with the cell
membrane or by endocytosis.
Most DNA viruses are entirely dependent on the host
cell's DNA and RNA synthesizing machinery,
and RNA processing machinery.
The viral genome must cross the cell's nuclear
membrane to access this machinery.

71. Replication cycle of A Virus
RNA viruses
These viruses are unique because their genetic
information is encoded in RNA.
Replication usually takes place in the cytoplasm.
RNA viruses can be placed into about four different
groups
depending on their modes of replication.

72. Replication cycle of A Virus
The polarity (whether or not it can be used directly to
make proteins) of the RNA
largely determines the replicative mechanism,
and whether the genetic material is single-stranded or
double-stranded.
RNA viruses use their own RNA replicase enzymes to
create copies of their genomes.

73. Replication cycle of A Virus
Reverse transcribing viruses
These replicate using reverse transcription,
which is the formation of DNA from an RNA template.
Reverse transcribing viruses containing RNA genomes
use a DNA intermediate to replicate,
whereas those containing DNA genomes use an RNA
intermediate during genome replication.
Both types use the reverse transcriptase enzyme
to carry out the nucleic acid conversion.
Retroviruses often integrate the DNA produced by reverse
transcription into the host genome.