Chapter 1
VIROLOGY: AN INTRODUCTION
ABSTRACT
The following chapter includes a brief introduction of the science of virology followed by an
early history and development of the concept of term virus. Viruses can be found everywhere in
nature and they have a ubiquitous nature. Viruses cannot be considered as organisms instead they
may be called as particles containing nucleic acids surrounded by protein coat. The structure and
classification of a virus has been discussed in this chapter. After reading this chapter you should
be able to comprehend the nature and structure of these small filterable particles known as
viruses.
INTRODUCTION TO VIROLOGY
Virology in general can be described as the study of small biological entities known as Viruses.
Essentially all the living organisms, when studied carefully, consists either of viruses as parasites
or viral genes incorporated in the genome of a living organism. Hence viruses; the smallest of
creatures have a great impact on the molecular mechanisms of a living organism. Since virology
has had a significant role on the study of biological processes of gene expression, cell growth,
cell development and mechanisms of genetic diversity; the study of viruses has enabled man to
understand the fundamentals of most of the modern biology, medicine and genetics that he
knows today.
Since viruses are parasitic in nature therefore the study of viral genome, viral processes of gene
expressions in host cells and viral replication provides fundamental information regarding the
cellular processes in general. The study of viruses, their genetics and mode of replication in
different hosts, specifically in bacteria has led to the major advancements and developments in
the fields of molecular biology as well as molecular genetics. For example when a virus infects
an individual by targeting specific tissues or cells, it elicits specific symptoms or immune
responses. In this way viral pathogenicity is defined and certain responses towards specific
viruses lead to better understanding of immune response and the precise molecular nature of cell
signaling pathways.[1]
As the science of virology is considered quiet vast, it cannot be defined immediately in just few
words or sentences. The central core around which the science of virology revolves; viruses, first
need to be defined and over the years many scientists have proposed many definitions for
viruses. The simplest of all definitions quoted by the author S. E. Luria states that “Viruses are
submicroscopic entities, capable of being introduced into specific living cells and of reproducing
inside such cells only”.
[2]
This definition gives us a practical as well as a restrictive aspect
towards the word virus clearly stating that these organisms are unable to replicate outside a
living host cell. We are not even sure if we can call viruses as “organisms” since they only
contain a genome surrounded by a protein coat and in some cases an envelope too. But what we
do know for sure is that they can be considered living particles as they consist of nucleic acids
i.e. either RNA or DNA.
Viruses differ from each other on various bases. They differ on the basis of type of host they
infect like there are animal viruses, plant viruses and even viruses specific for bacteria known as
bacteriophages. On the other hand viruses they may be distinguished from one another on the
basis of morphology, genome type or mode of replication. But there are some unifying principles
which all viruses follow and they are as follows [1, 3, 4]
1. Viral genome is always packaged inside the core of a particle in order to ensure safe
transfer from one host to another
2. In order to survive, all viruses establish themselves in a host population
3. The viral genome consists of all the information required for the initiation and
completion of an infectious cycle within a host cell that is rendered susceptible to that
specific infection
A BRIEF HISTORY OF VIRUSES
By the last half of 19th century, the fact that a vast variety of bacteria, protozoa and fungi exists
was already established. Jacob Henle of Gotingen was the first person to hypothesize that
infectious particles exist which are too small to be seen under the light microscope and which
might be involved in causing specific diseases. He made this hypothesis in around 1840 but due
to the absence of evidence, his idea of such entities got rejected.
[5]
In the late 19th and early 20th
century, medical science got so advanced that new experimental approaches were formulated due
to the contributions of well-known scientists such as Robert Koch (1843-1910) and Joseph Lister
(1827-1912). It was because of these scientists that the importance of sterile environment for
surgeries or for the isolation of new organisms was originated. The idea of solid media and
culture dilutions to obtain pure individual microbial colonies and staining methods for
identification were put together by Koch. Robert Koch put forth four major postulates to
establish a causative relationship between a microbe and a disease. These postulates state that (a)
the microorganism must be present in all organisms suffering from the disease and should not be
present on healthy individual; (b) The microorganism must be isolated from a diseased organism
and grown in pure culture; (c) When introduced into a healthy organism, cultured microorganism
should be able to cause disease; (d) the inoculated microorganism must be reisolated from
diseased experimental host and should be identical to the original causative agent. In light of
these postulates, for many years an infectious agent was not accepted as the cause of a disease
unless it met all the conditions mentioned above.[6] With the passage of time Koch himself and
many other scientists agreed to the fact that the four conditions cannot be met for all the disease
causing organisms. It was only when these rules broke down and scientists were unable to
establish a relationship between certain diseases and their agents, the concept of a virus was
born.
The initial discovery period of virus ranged between 1886 – 1903 during which three well
known scientists played a vital role in the development of new concept of the term „Virus‟. Adolf
Mayer (1843-1942) was the first scientist to have contributed in the development of this concept.
Although many scientists had already researched on diseases of tobacco, Mayer in 1879 also
started his research on different diseases of tobacco. On observing the light and dark spots on the
infected tobacco leaves, Mayer named the disease as “Tobacco Mosaic disease”. During his
various experiment on the disease Mayer found out that the infectious agent was being
consistently cultured and it was also able to fully transform a healthy plant into a diseased one
however Koch‟s postulates was also not being satisfied in such experiments. Mayer concluded
that the infectious particle could be a soluble, enzyme like contagium though he was not fully
satisfied with his own proposition. Finally Mayer concluded that the nature of the disease could
be bacterial however the infectious and life forms of such a bacterium are not yet known.
However a few years later Dimitri Ivanofsky (1864-1920) repeated Mayer‟s experiments with an
additional step of filtering the sap of infected plants. The Chamberland filter made of unglazed
porcelain was able to block the passage of bacteria resulting in bacteria free sap. In 1892,
Ivanofsky reported that the filtered sap of infected tobacco leaves retained their infectious
properties. This experiment came up with an operational definition of viruses i.e. an agent which
is smaller than bacteria and cannot be filtered could qualify as a virus.[5, 7]
Since Koch‟s postulates were still not being satisfied and most scientists at that time were bound
due to these four postulates, Ivanofsky proposed that this infectious particle could be a filterable
toxin. At that time another scientist who played a key role in developing the concept of a virus
was Martinus Beijerinck (1851-1931). Beijerinck was working in collaboration with Mayer and
was unaware of Ivanofsky‟s work. In 1998 with the help of his experiment Beijerinck found out
that when the filtered sap was diluted and inoculated into a healthy plant tissues, it could regain
its strength concluding that the infectious agent was certainly not a toxin as it had replicating
properties inside living host cells only. Beijerinck called the infectious agent “contagium vivum
flavidum” or in simple words a contagious living liquid. Thus the three scientists with their
experiments contributed to the idea of a filterable infectious particle too small to be seen under
light microscope and can only replicate in living host cells.[5, 7]
THE UBIQUITOUS NATURE OF VIRUSES
All cellular life forms such as eukaryotes and prokaryotes are host to viral infections. The viruses
can infecting prokaryotes are known as Bacteriophages or sometimes phages as well. A host
showing symptoms of disease confirms the presence of a virus in its cells. It is not necessary that
viruses will always cause a disease in its host cells. Many viruses are nonpathogenic to host in
which they reside. Some of these viruses are either active or inactive in their host cells. [8] If the
genome of a virus becomes incorporated into the host cell genome, it could be transferred to
generations over generations. This phenomenon of viral genome incorporation into host genome
has paved way for scientists in order to trace the origin of viruses. It has also been proposed that
the existence of viruses is as ancient as the existence of man himself. Apart from the living host
cells, viruses can also be found in air, soil, water. In general we can say that viruses are
everywhere. Aqueous environments contain a very high number of virus particles, some of
which also infect organisms living in those environments. An early discovering stating that there
are millions of microbes present in each milliliter of sea water but the question arise as to who
exactly eat those organisms. This question was then answered when the transmission electron
microsocope in 1989 was used and it was observed that there were around 10 million virus like
particles in one milliliter of seawater.[9] We should not be surprised to know that there are more
viruses known to infect mankind than any other species and new human viruses are still being
found and who knows how many are still out there which still needs to be discovered.
STRUCTURE OF VIRUSES
In general Viruses are small biological entities that are considered nonliving when outside the
body of a living organism but can infect and replicate themselves when they gain access to living
host cells. Viruses cannot be considered as cells but they are known as particles containing some
genetic material (typically RNA or DNA) surrounded by a protein coat known as a capsid.
Viruses existing as free particles outside a living host are known as Virions. The outer shell or
capsid of a virion has many shapes and sizes and are made up of proteins known as capsomeres.
The mere arrangement of capsomeres around the genetic material determines the shape of a
virion. However some viruses may also contain an outer layer which is known as the
envelope.[10]
Viruses are very small subcellular particles which are incapable to replicate outside a host cell
hence known as intracellular, obligate parasites. A viral assembly can incorporate only one of the
two types of nucleic acids i.e. either RNA or DNA which is then protected by a virus coded
protein coat. The nucleic acid carry all the genetic information necessary for the programming of
the synthetic machinery of host cell required for viral replication.[4] A virus is usually inert in
nature or in some cases it could be present in crystalline form. In order to carry out the process of
replication, viral particle or simply called virions need access to complex host biochemical
machinery. A virus particle only delivers its genome into the host cells and once viral genome is
expressed inside the host cell, further transcription and translation is then carried out by host cell
machinery. Therefore a virus is highly dependent upon its host for replication.
A fully assembled and infectious virus particle is considered as a virion. The major components
of a fully infectious virus particle are
1. Viral Genome
Viral genome consists of either type of two nucleic acids i.e. RNA or DNA
2. Capsid (Protein Coat)
Capsids are usually formed by the small repeating protein subunits into symmetrical
structures. These capsid proteins are coded by the viral genome and may be formed as
single or double protein shells consisting of one or a few structural protein species.[1, 3, 4]
Therefore the capsid protein components self-assemble in order to produce a complete
capsid structure. This self-assembly follows two basic patterns (a) helical or rod like
symmetry (protein subunits and nucleic acid arranged in a helix) and (b) icosahedral or
sphere like symmetry (protein subunits assembled in the form of a shell enclosing a
nucleic acid containing core). The size of a capsid plays a major role in dictating the
amount of genetic material to be packaged into the virus particle. The larger the size of a
capsid, the more amount of genetic material can be packaged and vice versa.[1, 3]
The two major functions of capsid are (a) protection of the viral genome from
extracellular environment and (b) attachment of a virion to host cell membrane
3. Envelope
Some of the virus families consist of an additional outer protective layer known as the
envelope. The envelope is usually derived from the host cell membranes during the
budding off process of virus particle. The lipid bilayer of viral envelope surrounds a shell
of membrane associated proteins which are encoded by virus itself. The outer layer of
envelope consists of trans-membrane proteins known as glycoproteins. These
glycoproteins play a role in viral attachment to host cell membrane and entry or uptake
by the host cell.[1, 4, 8]
CLASSIFICATION OF VIRUSES
The virus classification is based on its morphology, chemical composition and mode of
replication.
Morphology
Two basic types of morphological differences have been seen in different viral species known as
helical symmetry and icosahedral symmetry.
1. Helical Symmetry
During replication, the identical protein subunits (protomers) encoded by the viral
genome self-assemble in the form of a helical array. This helical array of identical
proteins surrounds the viral genome following a similar spiral path. These kinds of
nucleocapsids constitute firm, elongated rods or flexible filaments. These capsid
structures can be observed under an electron microscope.
2. Icosahedral Symmetry
A polyhedron having 20 equilateral triangular faces with 12 vertices is known as
an Icosahedron. When rotated within 360, a polyhedron repeats itself 5 times
about any of the fivefold axes. Likewise some viruses also constitute icosahedral
shapes in which the identical proteins known as protomers arrange themselves in
oligomeric clusters called as capsomeres. The capsomeres arrange themselves into
an icosahedral shell and the number and pattern of these capsomeres become the
basis for virus classification.
Chemical Composition and Mode of Replication
The viral genome may consist of either RNA or DNA which could be linear/ circular or single
stranded (ss)/ double stranded (ds). The entire genome may be present in a single molecule
known as monopartite genome or it may be present in several nucleic acid segments known as
multipartite genome. Replication strategies differ according to different types of viral genome.[4]
THE BALTIMORE CLASSIFICATION OF VIRUSES
The Baltimore system of virus classification was proposed by David Baltimore who named this
scheme after his own name. This system of classification is quite useful and it is based on the
central idea that all viral particles must first generate positive stranded mRNA in order to
produce proteins for replication. However the precise mechanisms of replication for each virus
differ. The various types of virus genomes can be broken down into seven different fundamental
groups. These seven groups have been summarized in the table given below
Table 1: Baltimore Classification of Viruses
Class
Nucleic Acid
ds DNA
I
II
ss DNA
III
ds RNA
IV
+ ss RNA
Example
Envelope
Herpesvirus
Yes
Poxvirus
Yes
Adenovirus
No
Papillomavirus
No
Adeno-associated
virus
No
Reovirus
No
Togavirus
Yes
Poliovirus
No
Hepatitis A virus
No
Hepatitis C virus
Yes
V
- ss RNA
Infulenza
Yes
VI
(reverse) RNA
HIV
Yes
VII
(reverse) DNA
Hepatitis B virus
Yes

ss = single strand; ds = double strand.

(+) RNA is the one which can function as mRNA for the synthesis of proteins. (-) RNA
cannot function as mRNA.
REFERENCES
1.
Wagner, E.K., et al., Basic Virology. 2009: Wiley.
2.
Luria, S., General Virology. 2011: BiblioBazaar.
3.
Flint, S.J., Principles of Virology: Molecular Biology, Pathogenesis and Control of
Animal Viruses. 2009: ASM.
4.
Baron, S., Medical Microbiology. 1996: University of Texas Medical Branch at
Galveston.
5.
Fields, B.N., D.M. Knipe, and P.M. Howley, Fields' Virology. 2007: Wolters Kluwer
Health/Lippincott Williams & Wilkins.
6.
Rivers, T.M., Viruses and Koch's postulates. Journal of bacteriology, 1937. 33(1): p. 1.
7.
Kung, S.D. and S.F. Yang, Discoveries in Plant Biology. 2000: World Scientific.
8.
Carter, J. and V.A. Saunders, Virology: Principles and Applications. 2007: Wiley.
9.
Breitbart, M. and F. Rohwer, Here a virus, there a virus, everywhere the same virus?
Trends Microbiol, 2005. 13(6): p. 278-284.
10.
Crawford, D.H., Viruses: A Very Short Introduction. 2011: OUP Oxford.