Download Influenza virus

The history of viruses dates back to 1670 when the
colour breaking of tulips was published in “Trait des
tulips”,
wherein
it
was
mentioned
that
the
color
variegation might be due to a disease. The first scientific
proof of the mosaic disease of tobacco came in 1892,
when Dimitry Iwanowisky proved that the infected sap
was capable of inducing the mosaic disease in healthy
plants, even after passing through bacterial- proof filter
candles. M W Beinerink1898 gave the name to this
infectious agent ‘contagium vivum fluidum’, and latter on
as filterable viruses. Meanwhile Bour and Beijerink coined
the term virus for this infectious agent.
The structural virology started only after the work of
Stanely who in 1935 isolated the tobacco mosaic virus in
crystalline form for which he was awarded the noble
prize. With the advancement of optical instrumentation,
structural and molecular virology gained momentum.
Characters of viruses
Lwoff and Tournier in 1966 described the following
characters of viruses:
Viruses posses only one type of nucleic acids either DNA
or RNA and never both;
virions reproduce from their sole nucleic acid;
virions are unable to grow or undergo binary fission;
they lack the genetic information for the synthesis of
Lipmann system; and
viruses make use of their host machinery (absolute
parasitism).
However, F C Bawden reduced the long list of characters,
defined viruses as “submicroscopic infective entities that
multiply
only
intracellularly
and
are
potentially
pathogenic.” Hahon in 1964 called these definitions as
orthodox and treated viruses as transmitters or vehicles
of information bearing genetic material and defined
viruses as “bits of infectious heredity in search of
chromosomes.” This definition seems to be relevant when
the
second
school
of
thought,
i.e.
“retrogressive
evolution of viruses” is taken into account.
General structure of viruses
Generally a virus consists of a strand of nucleic acid
surrounded
by
a
protein
coat;
hence
viruses
are
nucleoproteinacious. The whole virus particle is called
virion. The protein coat is known as capsid, and the
individual protein subunits are called capsomeres. The
nucleic
acid
together
with
protein
coat
is
called
nucleocapsid.
Therefore, viruses have three important components
which give them the structural organization and help in
its
replication
in
an
appropriate
host
cell.
These
components are:
Capsid
Genome
Envelope and enzymes
1. CAPSID
Capsid is a protein covering which encloses the
nucleic acid; hence capsid, along with the nucleic acid, is
called nucleocapsid. The proteins in the capsid are
arranged in smaller identical sub units, each unit is called
a
capsomere.
The
arrangement
of
capsomeres
is
characteristic for a particular virus. The capsomeres are
made up of monomers called protomers. There may be
similar or several types of protomers in the capsid.The
protomers are connected to one another with the help of
bonds. Protomers as well as capsomeres once exposed to
proper conditions, associate spontaneously to form the
capsid without any external help. This process is called
self- assembly. For example in tobacco mosaic virus
protomers aggregate to form a two layered disc. It is
followed by the association of code proteins with RNA at
a special site near 3end of the genome. RNA forms a loop
and inserts itself inside the hole of the disc. The
association of the protomers continues till the whole of
the RNA gets inserted in the capsid. The arrangement of
capsomeres in association with the nucleic acid gives a
definite symmetry to the virus particle. It may be helical
or polyhedral, and some viruses represent the both.
The capsid performs the following functions in a virus
particle:
1.
It protects the nucleic acid from any kind of damage
as a result of mechanical force, ultra-violet radiations
or due to the activity of host enzymes.
2.
It helps the virus in its attachment to a host cell with
specific receptors.
3.
It enables the virus particle to penetrate the cell
membrane of the host to inject the nucleic acid in
the host cytoplasm.
2. GENOME
Unlike other organisms, viruses show a great variation
in their genome. Primarily viruses posses either DNA or
RNA as their genetic material, but never both. It may be
single- stranded or double- stranded. It can be linear,
circular or segmented. The virus genome varies in size
from 3500 nucleotides to about 230 kbp (kilo base pairs).
With
the
advancement
in
the
molecular
biology
techniques, attention has been paid to explore the
genomic
composition
of
viruses.
The
following
generalizations may be made about the viral genome:
• Plant viruses usually contain RNA. It may be singlestranded
(ss
RNA)
or
double-
stranded
(ds
RNA).However, some plant viruses contain DNA.
(Table 02)
• Animal viruses generally contain double strandedDNA (ds DNA);however, some animal viruses posses
single- stranded RNA (ss RNA) and a few have
double- stranded RNA (ds RNA) (Tabl 01)
• Bacterial
virsuses
(Bacteriophages)
contain
DNA
(single stranded /double stranded) or RNA (single
stranded /double stranded) (Table 03)
(01) Adopted
(02)
Table 01. Animal viruses
02. Plant viruses
from
Presscort.
Table
(03)
Table 03 Bacterial viruses
2.1 RNA virus genome
As mentioned earlier that RNA genome is of two types:
Single- stranded RNA and
Double- stranded RNA
Single stranded RNA (ss RNA) virus genome
A single stranded RNA genome may be of plus (+) sense
i.e. with the same polarity as that of mRNA, negative (-)
sense incapable of gene expression or ambisense, i.e. a
mixture of both (+) and (-) sense.

Positive (+) sense single stranded RNA
The RNA of such viruses after uncoating in the cytoplasm
acts as mRNA and directs the synthesis of virus proteins
responsible for genome replication. Virus groups with
such
genomes
share
some
common
features,
for
example:
І. Purified (+) sense RNA can induce infection directly
without any virus protein.
П. Virus genome at its 5’ and 3’ ends posses an
untranslated region which do not code for any protein.
Ш. Both the ends are modified, 5 end by a methylated
nucleotide cap and 3 end by polyadenylation. The
modification helps the viral RNA in its recognition by
the host cell. The examples of ss + sense RNA viruses
are
Calciviruses,
Astroviruses
and
viruses,tobamoviruses and bromoviruses.
Picorna
 Negative (-) strand RNA Viruses
After uncoating of virus particle in the cytoplasm, the (-)
RNA strand remains associated with the transcriptase
enzyme
to
synthesize
an
mRNA
which
codes
for
structural proteins and enzymes that direct the synthesis
of + RNA. From + RNA more – RNA strands are
synthesised which act as genome for progeny viruses.
Rhabdoviruses, Paramyxoviruses and orthomyxoviruses
have (-) sense RNA. Rabies virus, tomato spotted wilt
virus, and potato yellow dwarf viruses are the common
examples.
 Ambisense genome organisation
Some viruses are partly + sense and partly – sense, e.g.
Arena viruses and some Buniya viruses.
o Double- stranded RNA virus genome
In case of animals only Reoviruses posses ds RNA, while
as in case of plants Partiviridae and Reoviridae posses ds
RNA. Wound Tumor and Rice Dwarf viruses are the
common examples.
2.2 DNA virus genomes
On the basis of the genome size the DNA genome of
viruses can be divided into two groups:
(a)Smaller DNA genome, and
(b)
Larger DNA genome.
o Smaller DNA genome
The best studied example of the smaller DNA genome is
that of bacteriophage M3. The genome of this virus is
circular with a single- stranded DNA and has about 7200
nucleotides. The double stranded- DNA
genome of
smaller size is that of phage lambda with 49 kbp and T4
Phage with a genome size of 160 kbp. The DNA is of
linear shape. In case of animal viruses, Parvo virus and
Polyoma viruses have smaller DNA genome. However
parvo virus is the only single- stranded DNA virus.
o Larger DNA genome
There is a large number of viruses whose genome is
double-
stranded
and
considerably
large.
The
genome of these viruses resembles that of the host
cellular genome in many respects, such as presence
of histone proteins, polyadenylation, and in presence
of split genes through coding and non coding
segments. Herpes virus and Adenoviuses are the
examples of viruses with large DNA genomes.
Herpes virus has a genome size of about 230 kbp
with linear double stranded DNA, while as that of
Adenovirus is 30-38 kbp in a linear form.
 Segmented and multipartite genome
When the genome is divided in to two or more
nucleic acid molecules and is packed in to a single
virus particle, the genome is said to be segmented.
Orthomyxoviruses, reoviruses and buniya viruses are
the
examples
of
segmented
virus
genomes.
Influenza virus has 8 RNA molecules with 890-2341
nucleotides. In case the genome is segmented but
packed into separate virus particles, it is said to be
multipartite. Such viruses can have two or three
capsids
and are accordingly called bipartite and
tripartite viruses. Multipartite genome is only found
in plant viruses, e.g. geminiviruses. In these viruses
genome is packed into many capsids.
3. Envelope and enzymes
Many viruses, those of plants, animals and bacteria
have
complex
membranous
structures
around
the
nucleocapsid, which is called envelope or peplos. The
virus
envelope
glycoproteins
consists
of
a
lipid
bilayer
with
embedded in it. Besides, there are
carbohydrates. The lipid and carbohydrates are derived
from the membranes of the host cell, whereas the
glycoproteins are of viral origin. Envelope sometimes give
rise projections which are called spikes or peplomers.
These structures help the virus in the attachment with
the host cell surface. Besides they are used as a
taxonomic tool in virus classification. Because of flexible
nature of envelope, enveloped viruses have a variable
shape and are called pleomorphic. However, in some
viruses the envelope is firmly attached to the capsid and
the viruses have a constant shape. Based on the
presence and absence of envelope, the viruses are
grouped as enveloped and non- enveloped viruses.
(Tables A & B)
DNA animal viruses
Non enveloped viruses
Parvovirus --- ss DNA
Enveloped viruses
hepadnavirus
---
partially
ds DNA
Papovirus --- ds DNA
Poxvirus--- ds DNA
Adenovirus ---ds DNA
Herpes virus --- ds DNA
Iridovirus---ds DNA
Table (A): Enveloped and non- enveloped DNA viruses
RNA: animal viruses
Non- enveloped viruses
Enveloped viruses
Picornavirus – ss RNA
Rhabdovirus – ss. RNA
Reovirus – ds RNA
Togavirus---ss RNA
Orthomyxovirus ---ss RNA
Bunyavirus ---ss RNA
Coronavirus ---ss RNA
Arenavirus ---ss RNA
Retrovirus---ss RNA
Paramyxovirus ---ss RNA
Table (B): Enveloped and non- enveloped RNA viruses
Influenza virus is a well- studied example of an
enveloped virus. (Fig.01 A, B). Spikes emerge out 10 nm
from the surface at about 7-8 nm intervals. These spikes
have enzymatic, absorptive, heamagglutinating and / or
antigenic activity. There are two types of spikes present
in influenza virus. These are called H.spikes and N.
spikes. N. spikes posses an enzyme called neuraminidase
(hence the name N. spike), which helps the virus in
penetrating
the
mucous
layers
of
the
respiratory
epithelium to reach the host cells. Besides neuraminidase
helps in assembly process and budding out of virus from
the host. Other spikes with hem-agglutinin proteins bind
the viruses to red blood cell membranes and cause hemagglutination.
Usually viruses lack enzymes, but still some viruses
do
have
enzymes
in
their
capsid
or
envelo,
e.g.
Neuraminidase in Influenza virus. Some enzymes are
involved in nucleic acid replication, e.g. RNA- dependent
RNA polymerase in Influenza virus, and RNA- dependent
DNA polymerase in HIV.
(a)
(b)
Fig.01. (a): An electron-micrograph of influenza virus
(b): Diagram of Influenza virus (Adopted
from Presscort, 2006)
 Symmetry of Viruses
Symmetry refers to any structure, which when rotated
around an axis so that the same form is seen from all
sides.The morphology of virus is determined by the
arrangement of protomers (protein morphological units).
Primarily, viruses have two kinds of symmetries, viz.
spherical or icosahedral and helical or rod shaped.
However, some viruses have binal symmetry, i.e. they
are partly helical and partly icosahedral. Therefore,
viruses occur in three main shapes viz, icosahedral,
helical and complex.
o
Icosahedral or polyhedral symmetry
When protomers aggregate into units of five or six
capsomeres, they condense to form an icosahedrons,
with 20 faces of equilateral triangles and 20 apices.
Pentamers
or
pentons
are
at
the
vertices
of
the
icosahedrons and hexamers or hexons form edges and
triangular faces. Viruses with such a type of symmetry
are called icosahedral or polyhedral. The number of
capsomeres in an icosahedron varies from virus to virus,
e.g. ф X 174 has 12 capsomers, turnip yellow mosaic
and polio viruses have 32 each, polyoma virus has 72,
herpes virus has 162, and adeno viruses have 252
capsomeres.
A common example of an icosahedron is the Adeno virus,
whose detailed structure is discussed here. (Fig.2 A,B).
The Adenoviruses are DNA- containing viruses, which
cause mild respiratory infections in humans. Some
adenoviruses cause tumors in animals. The virus has a
diameter of 75 nm and its coat consists of 11 to 15
distinct proteins. The major coat proteins are called
hexons and constitute the major proteins of the faces of
the icosahedrons. The hexons are actually trimers,
composed of three identical polypeptides. At the five
vertices of the icosahedrons are 12 pentons. Some
characteristic fibers are attached to the pentons, which
help the virus particle in its attachment with the host cell.
The moleculer weight of the DNA is 20 × 10⁶ Daltons.
(A)
(B)
Fig.02 (A) A model of an icosa hedral capsid (Adeno
Virus)
(B) An electron micrograph of Adeno virus. (Adopted
from
M.T. Madigan)
o
Helical Symmetry
When the protomers are arranged in such a way that
they form a long rigid hollow tube, the virus symmetry is
said to be helical. Tobacco Mosaic Virus (TMV) is the best
studied example of helical capsid (fig. 03 A, B).
TMV is an RNA virus about 150 A° thick and 3000 A°
long, with a central hole of 40 A°. The capsid is
composed of 2130 identical protein subunits, with a
molecular weight of 17000 daltons. Each subunit has 158
amino acids. The helix has 16⅓ subunits per turn. There
are 130 turns along the helix. The length of the helical
viruses is determined by the length of the nucleic acid.
The nucleic acid in TMV is a single stranded RNA molecule
coiled into a helix and has a diameter of 80 A°. RNA helix
has 49 nucleotides with a pitch of 23 A°. There are 6400
nucleotides with a molecular weight of 2× 10⁶ Daltons.
(A)
(B)
Fig03:A. - A model of T.M.V. Helical array of
protomers with RNA coiling
B. - An electron micrograph of
T.M.V at high resolution power (courtesy J.T. Finch)
Adopted from
Presscort
o
Complex Symmetry
Some viruses do not fit in to the helical or icosahedral
symmetries, but rather show a combination of both and,
therefore, have a binal symmetry. Pox viruses and
bacteriophages are the common examples of complex
viruses. The structure of bacteriophage T4 will be
discussed here in detail. The bacteriophage is tadpole
like, with a polyhedral head and a cylindrical tail. The
head is an icosahedron elongated by one or two rows of
hexamers in the middle. It has a diameter of 96 X 65 nm,
and is made up of 2000 similar protein subunits, and
contains a circular double-stranded DNA about 53µm
long. The tail has helical symmetry. It is attached with
the head by means of a collar or neck piece. It has a
central hollow tube, a sheath surrounding the tube and a
complex base plate. The sheath is made up of 144
protein subunits arranged in 24 rings and each ring made
of six protein subunits. The base plate is hexagonal and
has a pin and a jointed tail fiber at each corner. The
length of the tail fiber is 130 A°. The tail fibers are the
organs of attachment to the specific sites of the host cell
(Fig 04 A, B)
(A)
Fig04:A.—Diagramatic
(B)
representation
bacteriophage. Source: Presscort
of
T-even
B. --- An Electron micrograph of T. even
Bacteriophage. Source: Madigan