Viruses

*infectious agent of small size and simple composition that can multiply
only in living cells of animals, plants, or bacteria. The name is from a Latin
word meaning “slimy liquid” or “poison.”
* Viruses are submicroscopic, obligate intracellular parasites. Most are too
small to be seen by optical microscopes, and they have no choice but to
replicate inside host cells.
*Viruses are have no cell nucleus cytoplasm or organelles and particles
contain only one nucleic acid either DNA OR RNA but never both .
*Viruses show property of living things only inside a living cell and out
side the cell they be have like a nonliving thing
• Virus particles (virions) do not grow or undergo division
*Virus is not a problem to differentiate viruses from multicellular organisms
such as plants and animals. Even within the broad scope of microbiology,
covering prokaryotic organisms as well as microscopic eukaryotes such as algae,
protozoa, and fungi, in most cases this simple definition is enough.

*A few groups of prokaryotic organisms also have specialized intracellular

parasitic life cycles and overlap with this description. These are the Rickettsiae
and Chlamydiae-obligate intracellular parasitic bacteria which have evolved to
be so cell-associated that they can exist outside the cells of their hosts for only a
short period of time before losing viability.
*Viruses are also found in soil air and water many aqueous environments
contain very high concentrations of viruses that infect the organisms that live in
those environments.
A common mistake is to say that viruses are smaller than bacteria. While this is
true in most cases, size alone does not distinguish them.

Most viruses vary in diameter from 20 nanometres to 250–400 nm; the largest,
however, measure about 500 nm in diameter and are about 700–1,200 nm in
length. Only the largest and most complex viruses can be seen under the light
microscope at the highest resolution.

The largest virus known (currently Pithovirus sibericum) is 1,200 nm long, while
the smallest bacteria (e.g., Mycoplasma) are only 200 - 300 nm long. Nor does
genetic complexity separate viruses from other organisms.
• The largest virus genome (Pandoravirus, 2.8 Mbp—million base pairs—
approximately 2,500 genes) is twenty times as big as smallest bacterial
genome (Tremblaya princeps, at 139 kbp—thousand base pairs—and
with only 120 protein coding genes), although it is still shorter than the
smallest eukaryotic genome (the parasitic protozoan Encephalitozoon,
2.3 Mbp).
• For these reasons, it is necessary to go further to produce a definition
of how viruses are unique
• Host range and distribution

• Logic originally dictated that viruses be identified on the basis of the

host they infect. This is justified in many cases but not in others, and
the host range and distribution of viruses are only one criterion for
their classification. It is still traditional to divide viruses into three
categories: those that infect animals, plants, or bacteria.

• Virtually all plant viruses are transmitted by insects or other

organisms (vectors) that feed on plants. The hosts of animal
viruses vary from protozoans to humans. Many viruses infect either
invertebrate animals or vertebrates, and some infect both. Certain
viruses that cause serious diseases of animals and humans are carried
by arthropods. These vector-borne viruses multiply in both the
invertebrate vector and the vertebrate host.
 Structure of virus :
(1) - A nucleic acid
)2( - capsid
)3(- Envelope (some but not all viruses)

• The nucleic acid

• As is true in all forms of life, the nucleic acid of each virus encodes the
genetic information for the synthesis of all proteins. In almost all free-
living organisms, the genetic information is in the form of double-
stranded DNA arranged as a spiral lattice joined at the bases along the
length of the molecule (a double helix).
• In viruses, however, genetic information can come in a variety of
forms, including single-stranded or double-stranded DNA or RNA. The
nucleic acids of virions are arranged into genomes. All double-
stranded DNA viruses consist of a single large molecule, whereas
most double-stranded RNA viruses have segmented genomes, with
each segment usually representing a single gene that encodes the
information for synthesizing a single protein.
• Viruses with single-stranded genomic DNA are usually small, with
limited genetic information. Some single-stranded DNA viruses are
composed of two populations of virions, each consisting of
complementary single-stranded DNA of polarity opposite to that of
the other
Capsid :

Capsids are constructed from many molecules of one or a few species •

of protein. The individual protein molecules are asymmetrical, but
they are organized to form symmetrical structures. A symmetrical
object, including a capsid, has the same appearance when it is rotated
through one or more angles, or when it is seen as a mirror image. For
the vast majority of viruses the capsid symmetry is either helical or
icosahedral
Figure 8:
Symmetrical structures. All these types of symmetry are seen amongst
viruses. The most common are helical and icosahedral symmetries.
• Capsids with helical symmetry

• The capsids of many ssRNA viruses have helical symmetry; the RNA is
coiled in the form of a helix and many copies of the same protein
species are arranged around the coil (Figure 9 a, b). This forms an
elongated structure, which may be a rigid rod if strong bonds are
present between the protein molecules in successive turns of the
helix, or a flexible rod (Figure 9 c) if these bonds are weak.

• For many ssRNA viruses, such as measles and influenza viruses, the
helical nucleic acid coated with protein forms a nucleocapsid, which is
inside an envelope The nucleocapsid may be coiled or folded to form
a compact structure
Figure 9:
Helical symmetry. (a) Structure of a capsid with helical symmetry. The ssRNA coils are coated with repeated copies of a
protein. (b) Part of measles virus nucleocapsid. The complete nucleocapsid is folded and enclosed within an envelope.
Reconstructed image from cryo-electron microscopy, (c) Beet yellows virus particle. The virion is a long flexible rod, at
one end of which there is a ‘tail’ (arrow) composed of a minor capsid protein, detected here by specific antibodies
labelled with gold.
• Capsids with icosahedral symmetry

• Before proceeding further, a definition of the term ‘icosahedron’

is required. An icosahedron is an object with
• • 20 faces, each an equilateral triangle;
• • 12 vertices, each formed where the vertices of five triangles meet;
• • 30 edges, at each of which the sides of two triangles meet.
• An icosahedron has five-, three- and two-fold axes of rotational
symmetry (Figure 12).
• Capsids with icosahedral symmetry consist of a shell built from
protein molecules that appear to have been arranged on scaffolding
in the form of an icosahedron. They have less contact with the virus
genome than the capsid proteins of viruses with helical symmetry.

• To construct an icosahedron from identical protein molecules the

minimum number of molecules required is three per triangular face,
giving a total of 60 for the icosahedron (Figure 13 a). The capsid of
satellite tobacco mosaic virus is constructed in this way (Figure 13 b).
 Figure 13:
Capsid constructed from sixty protein
molecules. (a) Arrangement of protein
molecules, with three per triangular face. (b)
Figure 12: Virions of satellite tobacco mosaic virus. The
The three axes of bar represents 5 nm.
symmetry of an icosahedron.
• The capsids of many icosahedral viruses are composed of more than
one protein species. That of cowpea mosaic virus is composed of two
proteins (Figure 14): one is present as ‘pentamers’ at the vertices of
the icosahedron (12 × 5 = 60 copies) and the other is present as
‘hexamers’ on the faces. Each ‘hexamer’ is composed of three copies
of a protein with two domains. The arrangement is similar to that of
the panels on the surface of the football.

• There is a huge range in the sizes of virus genomes, with all the large
genomes being dsDNA. There is also a huge range in the sizes of
icosahedral capsids
Figure 14:
Capsid constructed from two protein species. The
cowpea mosaic virus capsid is constructed from one
protein species (blue) that forms 12 ‘pentamers’, and
from a second protein species with two domains
(green and red) that forms 20 ‘hexamers’. The
football is similarly constructed from 12 ‘pentamers’
and 20 ‘hexamers’. The cowpea mosaic
• Capsomeres
• The capsids of some viruses, such as papillomaviruses, are clearly
constructed from discrete structures. These structures are called
capsomeres and each is built from several identical protein
molecules.

• The capsids of papillomaviruses are constructed from 72 capsomeres,

which are all identical, but the capsids of some viruses are
constructed from two types of capsomere: pentons, which are found
at the vertices of the icosahedron, and hexons, which make up the
remainder of the capsid. In these viruses there are always 12 pentons
(one at each vertex), but the number of hexons varies; for example,
the capsids of herpesviruses and adenoviruses contain 150 and 240
hexons, respectively
Envelope:
Some viruses also have a lipid membrane known as an envelope .virus
envelope can be external surrounding the entire capsid or internal
found beneath the capsid
Viruses with only a capsid and no envelope are known as naked or
nonenveloped viruses
Theses surface projective are glycoproteins that serve to attach virions
to specific receptor sites on host cell surfaces
In ceryain viruses the possession of spikes causes various types of rod
blood cells to clump or hemagglutinate a property useful in viral
identification
• The criteria used for classifying viruses into families and genera are
primarily based on three structural considerations:
(1) the type and size of their nucleic acid,
(2) the shape and size of the capsids, and
(3) the presence of a lipid envelope, derived from the host cell,
surrounding the viral nucleocapsid
Virus genomes
A virion contains the genome of a virus in the form of one or more molecules of nucleic acid.
For any one virus the genome is composed of either RNA or DNA. If a new virus is isolated,
one way to determine whether it is an RNA virus or a DNA virus is to test its susceptibility to a
ribonuclease and a deoxyribonuclease. The virus nucleic acid will be susceptible to
degradation by only one of these enzymes.

Each nucleic acid molecule is either single-stranded (ss) or double-stranded (ds), giving four
categories of virus genome: dsDNA, ssDNA, dsRNA and ssRNA. The dsDNA viruses encode
their genes in the same kind of molecule as animals, plants, bacteria and other cellular
organisms, while the other three types of genome are unique to viruses. It interesting to note
that most fungal viruses have dsRNA genomes, most plant viruses have ssRNA genomes and
most prokaryotic viruses have dsDNA genomes. The reasons for these distributions
presumably concern diverse origins of the viruses in these very different host types.
Fig 1:
Linear and circular viral genomes.
ss: single-stranded ds: double-stranded
There are no viruses known with circular dsRNA genomes
RNA virus genomes
 • Classification of virus
• Viruses are mainly classification phenotypic characteristics ,such as
morophology, nucleic acid type ,mode of replication ,host organisms,
and the type of disease they cause.
• Currently there are two main schemes used for the classification of
viruses:
• 1- The international committee on taxonomy of viruses (ICTV)system
• 2- The Baltimore Classification system.
• ICTV system of classification
• the international committee on taxonomy of viruses (ICTV) was
established in 1966 to provide a single taxonomic scheme for viral
classification and identification
• For most virueses, order an families are the highest taxonomic groups
established so far by ICTV.
• Family names are typically , derived from special characteristics of
viruses within the family or from the name of an important member
of the family eg. Picornaviridae , Hepadnaviridae, herpesviridae.
• Viruses are assigned to certain genera viruses at the species level:
but given common english designations
 • Classification of virus
• Viral classification starts at the level of order and follows as thus with the
taxon suffixes given in italics :
• Order (- virales)
• Family (- viridae)
• Subfamily (- virinae)
• Genus (- virus)
• Species

• So far six orders have established by the ICT: the Caudovirales ,Herpesvirales
Mononegavirales, Nidovirales,Picornavirales,and Tymovirales
• These orders span viruses with varying host ranges :
• Caudovirales are tailed ds DNA (groupI) bacteriophages.
• Hepesvirales contains large eukaryotic ds DNA viruses
• Mononegavirales includes non –segmented (-) strand ssRNA (groupV)
Plant and animal viruses
• Nidovirales is composed of (+) strand ssRNA (groupIV) virses with
vertebrate hosts ,family of Coronaviridae viruses (SARS –COV2 viruses)
• Picornavirales contains small (+) strand ssRNA viruses that infect a
variety of plant insect ,and animal hosts.
• Tymovirales contains monopartite ssRNA viruses that infect plants
• Baltimore classification
• First defined in 1971 - a classification system that places viruses into one of
seven groups depending on a combination of their nucleic acid (DNA OR RNA)
strandedness (single-stranded or double- stranded), sense and method of
replication
• These groups are designates by ROMAN NUMERALS and discriminate viruses
depending on their mode of replication , and genome type
I. ds DNA viruses
II. ss DNA viruses
III. ds RNA viruses
IV. (+) ss RNA viruses
V. (-) ss RNA viruses
VI. ss RNA-RT viruses
VII. ds DNA –RT viruses
 DNA VIRUSES

DOUBLE –STRANDED SINGLE –STRANDED

Unenveloped
Enveloped Unenveloped

Hepadnaviruses Adenoviruses Parvoviruses

Herpesviruses Papillomaviruses
A poxviruses Polyomaviruses
 RNA VIRUSES

+RNA (-)RNA (+/-) RNA (+)RNA VIA DNA

ds

ENVELOPED UNENVELOPED ENVELOPED Double capsid ENVELOPED

Coronaviruses Arenaviruses (s)

Caliciviruses
Faviviruses Bunyaviruses (s) Reoviruses (s) Retoviruses
Picomaviruses
Togaviruses Filoviruses
Orthomyxoviruses(s)
Paramyxoviruses
Rhabdoviruses
• Positive sense and negative sense DNA refer to the coding sequence and non-
coding sequence (template) respectively.
• If a DNA sequence directly gives the same mRNA sequence from the
transcription ,it is known as positive sense or sense DNA ,IF a DNA sequence
Prouduces compementary m RNA sequence from the transcription , it is
known as negative sense or antisense DNA .
The genome of an RNA virus is referred to as either positive sense or negative
Sense.
Positive sense RNA virus possesses a single –stranded RNA genome that can
work as mRNA sequence and directly translate to produce the amino acid
Sequence. Negative sense RNA virus contains a single – stranded RNA genome
That prouduces complementary mRNA sequence from the transcription.
 Viral infection
• The viral infection that many are using your cells make more copies of
themselves
1- Attachment 2- Enter
3- Genome replication and gene expression 4-Assembly
5- Release
The viral lifecycle is the set of step in which a viral recognizes and
enters a host cell reprograms the host by providing instructions in the
from viral DNA or RNA and uses the host resources to make more virus
particles.
• 1- Attachment : the virus recognizes and binds to a host cell via a
receptor molecule on the cell surface
• 2- Enter :the virus or its genetic material enters the cell
• 3- Genome replication and gene expression :the viral genome is copied
and its gene are expressed to make viral proteins
• 4- Assembly : new viral particles are assembled from the genome copies
And viral proteins
• 5- Release :completed viral particles exit the cell and can infect other cells
 Attachment
• In attachment a specific protein on the capsid of the virus physically
sticks to a specific molecule on the membrane of the host cell
• This molecule called a receptor is usually a protein a virus recognizes
its host cells based on the receptors they carry and a cell without
receptors for a virus cant be infected by that virus
 2-Entry
• On typical route for viral entry is fusion with the membrane which is
most common in viruses with envelopes viruses may also trick the
into taking them in by a bulk transport process called endocytosis
some even inject their DNA in the cell
 Genome replication and gene expression
• involves copying the viral genome and making more viral proteins so
that particles can be assembled
• The materials for these processes (such as nucleotides)come from the
host cell not the virus
• Most of the machinery for replication and gene expression is also
provided by the host cell
• For instance the messenger RNAs (mRNAs) encoding viral genes viral
translated into viral proteins using the host cells ribosome
• However certain steps such as the copying of an RNA virus must encode
their own enzymes
• All viruses must encode capsid proteins and enveloped viruses typically
also encode envelope proteins (which often aid in host recognition)
• Viruses may also encode proteins that manipulate the host genome (e.g
blocking host defenses or driving expression of genes to benefit the virus)
Help with viral genome replication or play a role in other parts of the
lifecycle
 Assembly
• Newly synthesized capsid proteins come together to from capsomers
which interact with other capsomers to from the full-sized capsid.
• Some viruses like head –tail viruses first assemble an empty capsid and
then stuff the viral genome inside
• Other viruses build the capsid around the viral genome as shown below
 Release
• The last step in the virus lifecycle is the release of newly made viruses
from the host cell
• Different types of viruses exit the cell by different routes some made host
cell burst a process called lysis which others exit through the cell own
export pathways exocytosis and others yet bud from the plasma
membrane taking a patch of it with them as they go
• In some cases the release of the new viruses kills the host cell (for
instance a host cell that bursts will not survive) in other cases the exiting
viruses leave the host cell intact so it can continue cranking out more virus
particles.