Bacteriophage is the most common and extensively studied virus. The life cycle of bacteriophages. The transfer of their genetic system via the process of transduction (Generalised and Specialised) and studying the gene mapping in phages. This theoretical explanation about viruses and their genetic system will help the learner in the fields of biotechnology, microbiology, basic science, life science, and various other fields of biology.

1. VIRUSES AND THEIR
GENETIC SYSTEM
PRESENTED BY:

2. SONAL SINGH SHRIVAS
SYNOPSIS
Introduction
Discovery
Viral structure
Shape and size of the virus
Classification of viruses
1.Bacterial virus
 Bacteriophage virus
 Phage genome
 Life cycle of bacteriophage
(i) Lytic cycle
(ii) Lysogenic cycle
 Techniques for studying bacteriophages
 Transduction
(i) Generalized transduction
(ii)Specialized transduction
 Gene mapping in phages
 Fine structureanalysis if bacteriophage gene
Benzer’s mapping techniques
2.RNA and retrovirus
3.Animal virus
4.Plant virus

3. Other viruses and disease caused by them
Latest studies
INTRODUCTION
 All organisms—plants, animals, fungi, and bacteria—are infected by
viruses.
 A virus is a simple replicating structure made up of nucleic acid
surrounded by a protein coat.
 In other words, viruses are simple, non-cellular entities consisting of one
or more molecules of either DNA or RNA enclosed in a protein coat.
 They reproduce only within the living cells and are therefore, known as
obligate intracellular parasites.
 A fully assembled infectious virus is called a virion.
 The main function of the virion is to deliver its DNA or RNA genome
into the host cells so that the genome can be expressed by the host cells.
 Each viral species has a very limited host range; i.e, it can reproduce in
only a small group of closely related species.
 But unlike, simpler infectious agents, viruses contain genes, which give
them the ability to mutate and evolve.
 There are about 15 million different species of viruses have been
estimated in our planet, but only 2 million of them are currently known
to science.
DISCOVERY
 In 1884, the French Microbiologists CHARLES CHAMBERLAND
invented a filter, today known as the CHAMBERLAND FILTER or
CHAMBERLAND-PASTEUR FILTER, that has pores smaller than
bacteria. Thus he could pass a solution containing bacteria through the
filter and completely remove them from the solution.
 In early 1890s, the Russian biologists DMITRI IVANOVSKY used this
filter to study what came to be known as Tobacco Mosiac Virus. His

4. experiments showed that extracts from the crushed leaves of the tobacco
plants remain infectious after filtration.
 In 1899, a Dutch microbiologists MARTINUS BEIJERNICK
observed that the agent multiplied only in dividing cells. Having failed
to demonstrate its particulate nature he called it “contagium vivum
fluidium”, which means “a soluble living germ.”
 In the early 20th
century, the English bacteriologist FREDRICK
TWORT discovered viruses that infect bacteria (Bacteriophages).
 With the invention of electron microscope in 1931 by the German
engineers ERNST RUSKA and MAX KNOLL came up with the first
image of viruses.
 In 1935, American biochemist and virologists WENDELL
MEREDITH STANLEY examined the tobacco mosaic virus and found
it to be mostly made up of proteins. After sometime this virus was
separated into protein and RNA parts.
 The breakthrough came in 1931, when the American pathologist
ERNEST WILLIAM GOODPASTEUR grew influenza and several
other viruses in fertilized chicken’s eggs.
VIRAL STRUCTURE
 The structure of virions are very diverse, varying widely in size, shape
and chemical composition.
 All viruses have a nucleocapsid composed of nucleic acid surrounded by
a protein capsid.
 Capsids are formed as single or double protein shells and consist of only
one or a few structural protein species. The proteins used to build the
capsid are called capsomers.
 The nucleic acid together with the capsid forms the nucleocapsid.
 Some viruses have a membranous envelope that lies outside the
nucleocapsid.
 Those virions having an envelope are called enveloped viruses,
whereas

5.  Those lacking an envelope are called naked viruses (or non-
enveloped viruses).
 The genome of virus may consis of DNA or RNA, which may be single-
stranded (ss) or double-stranded (ds), linear or circular.
 Single-stranded RNA genomes can be either Plus (+) sense or minus (-)
sense.
SHAPE AND SIZE
SIZE

6. Viruses are smaller than prokaryotic cells (such as bacteria) ranging in size
from 0.02- 0.3 m.
Viral genomes are smaller in size. The largest known viral genome is of
bacteriophage G (670kbs).
SHAPE
All viruses have nucleocapsid (nucleic acid and protein) structure. The
symmetry refers to the way in which the capsomers are arranged in the virus
capsid.
They may be of the following types:
1. ICOSAHEDRAL:
 It is characteristic of the nucleocapsids of many spherical viruses.
 An icosahedrons is a regular polyhedron with 20 equilateral
triangular faces and 12 vertices.
 Example- Adenovirus.
2. HELICAL:
 It is seen in nucleocapsids of many filamentous and pleomorphic
viruses.
 Helical nucleocapsids consist of a helical array of capsomers
wrapped around a helical filament of nucleic acid.
 Example- Tobacco mosaic virus.
3. HEAD-TAIL:
 These capsids are a kind of hybrid between the helical and
icosohedral shapes.
 They basically consists of a icosahedral head attached to a
filamentous tail.
 Example- Bacteriophage virus.

7. SHAPE AND SIZES OF SOME COMMON VIRUSES ARE GIVEN
BELOW:
NAME OF THE
VIRUS
SIZE (in kb) SHAPE
Picorna virus 7-8 kb Icosahedral
Orthomyxo virus 10-15 kb Helical
Parvo virus 4-6 kb Icosahedral
Adenovirus 28-45 kb Icosahedral
Poxvirus 130-375 kb Complex
CLASSIFICATION OF VIRUSES
Viruses are classified into different taxonomic groups based on their host,
virion structure and composition, mode of reproduction, and the nature of any
disease caused.
Currently, viruses are classified with a taxonomic system placing primary
emphasis on the host, type and strandedness of viral nucleic acids, and on the
presence or absence of an envelope.
Based on the nature of the host, viruses mainly are classified into:
 Bacterial virus
 Animal virus
 Plant virus, etc.

8. BACTERIOPHAGE (Bacterial virus)
 Bacteriophages are the viruses that infect bacteria.
 They were first observed in 1915 by F.Twort in England and in 1917
by F. d’Herelle in France.
 D’Herelle coined the term “Bacteriophage”- eaters of bacteria.
 Several morphologically distinct types of phages have been described,
including polyhedral, filamentous, and complex.
 Complex phages have polyhedral heads to which tails and sometimes
other appendages (tail plates, tail fibers) are attached.
PHAGE T4
T4 is an example of complex phage.
 It contains a linear double-stranded DNA genome (172 kb) enclosed in a
capsid and attached to a tail.
 The T4 capsid is an elongated icosahedrons.
 It has a very elaborate tail structure including a collar at the base of the
head and a rigid tail core surrounded by a contractile sheath.
 The core and sheath are attached to a hexagonal base plate.
 Attached to the tall plate are tail pins and six kinked tail fibers.

9. LIFE CYCLE OF BACTERIOPHAGE
All phages must carry out a specific set of reactions in order to make more
copies of themselves.
The Bacteriophage have two alternative life cycles:
1.Lytic cycle
2.Lysogenic cycle
THE LYTIC CYCLE:
Lytic or vegetative life cycle culminates in the lysis (rupture) of the host cell
and the release of numerous viral progeny.
Bacterial viruses exhibiting a lytic life cycle are also known as virulent
bacteriophages (or lytic phages) because they inevitably cause the death and
destruction of the host bacterium. Example- T-even phages.

10. The lytic cycle consists of five steps:
1. ATTACHMENT: The bacteriophage binds to the specific host cell
molecules (receptors) on the bacterial cell wall.
2. PENETRATION: After the virus attaches to its host, it introduces its
genetic material (DNA) into the cell cytoplasm.
3. DNA COPYING AND PROTEIN SYNTHESIS: Once the
bacteriophage genome enters the cytoplasm, it subverts the host’s
nucleic acid (DNA) and protein synthesis apparatus and initiates the
synthesis of the viral proteins and DNA.
4. ASSEMBLY: After viral protein synthesis, they self-assemble into viral
components such as the head (containing the phage DNA), tail, and tail
fibers. The assemble process results in the formation of numerous intact
phage particles within the cell.
5. LYSIS: After the assembly step is completed, viral proteins cause the
lysis of the host cell, and all the viral progeny are released into the
environment.
LYSOGENIC CYCLE
In the lysogenic cycle, the viral DNA is inserted into the host’s DNA and
replicates as the host’s DNA replicates without killing its host. A lysogenic
virus (template) can remain in this state for numerous replications of the host
cell DNA until it excises itself from the host DNA and undergoes a lytic life
cycle.

11. When the genetic material of these phages is inserted into the DNA of the host
cells, it is said to be in the prophage state. A cell that contains a prophage is
known as a lysogen.
When a cell becomes lysogenized, occasionally extra genes carried by the
phage get expressed in the cell. These genes can change the properties of the
bacterial cell. This process is called lysogenic or phage conversion.
Example: Bacteriophage of E.coli lambda (
The lysogenic cycle consists of the following steps:
1. The lysogenic cycle begins like the lytic cycle, but inside the cell, the
phage DNA integrates into the bacterial chromosome, where it remains
as inactive prophage.
2. The prophage is replicated along with the bacterial DNA and is passed
on when the bacterium divides.
3. Certain stimuli cause the prophage to dissociate from the bacterial
chromosome and enter into the lytic cycle, producing new phage
particles and lysing the cell.
TECHNIQUES FOR STUDY OF BACTERIOPHAGES
 Viruses reproduce only within host cells, so bacteriophages must be
cultured in bacterial cells.
 For this, phages and bacteria are mixed together and plated on solid
medium on a petri plate.

12.  A high concentration of bacteria is used so that the colonies grow into
one another and produce a continuous layer of bacteria, or “lawn,” on
the agar.
 An individual phage infects a single bacterial cell and goes through its
lytic cycle.
 Many new phages are released from the lysed cell and infect additional
cells, the cycle is then repeated.
 Because the bacteria grow on solid medium, the diffusion of the phages
is restricted and only nearby cells are infected.
 After several rounds of phage reproduction, a clear patch of lysed cells,
or plaque, appears on the plate.
 Each plaque represents a single phage that multiplied and lysed many
cells. Plating a known volume of a dilute solution of phages on a
bacterial lawn and counting the number of plaques that appear can be
used to determine the original concentration of phage in the solution.
Plaquesare clear patchesof lysed cells on a lawn of bacteria.

13. TRANSDUCTION
Transduction is a method of gene transfer in bacteria from donor to recipient
using bacteriophage virus. In transduction at first bacteriophage infects donor
bacteria and then carries some part of donor genome with it. When this
bacteriophage infects new bacterial cell, it transfer that DNA in to recipient
cell.
There are two types of transduction:
1. GENERALIZED TRANSDUCTION:
 JOSHUA LEDERBERG and NORTON ZINDER discovered
generalized transduction in 1952, while trying to produce recombination
in the bacterium Salmonella typhimurium by conjugation.
 If all the fragments of donor DNA from any region of chromosome have
a chance to enter into transducing bacteriophage then it is known as
generalized transduction.
 In this type of transduction, a bacterial host cell is infected with either a
virulent or a temperate bacteriophage engaging in the lytic cycle of
replication.
 After the first three steps of replication (absorption, penetration, and
synthesis), the virus enters into the assembly stage, during which fully
formed virions are made.
 During this stage, random pieces of bacterial DNA are mistakenly
packaged into a phage head, resulting in the production of
a transducing particle.
 While these particles are not capable of infecting a cell in the
conventional sense, they can bind to a new bacterial host cell and inject
their DNA inside. If the DNA (from the first bacterial host cell) is
incorporated into the recipient’s chromosome, the genes can be
expressed.

14. 2. SPECIALIZED TRANSDUCTION:
 In specialized transduction, bacteriophage transfer only a few restricted
gene (DNA fragments) from donor bacteria to recipient bacteria.
 Specialized transduction can only occur with temperate bacteriophage,
since it involves the lysogenic cycle of replication.
 At first temperate bacteriophage enter into donor bacteria and then its
genome gets integrated with host cell’s DNA at certain location and
remains dormant and pass generation to generation into daughter cell
during cell division.
 When such lysogenic cell is exposed to certain stimulus such as some
chemicals or UV lights, it causes induction of virus genome from host
cell genome and begins lytic cycle.
 On induction from donor DNA, this phage genome sometimes carries a
part of bacterial DNA with it. The bacterial DNA lies on sides of
integrated phage DNA are only carried during induction.
 When such bacteriophage carries a part of donor bacterial DNA infects a
new bacteria, it can transfer that donor DNA fragments into new
recipient cell. So, in this specialized transduction only those restricted

15. gene are situated on the side of integrated viral genome have a chance to
enter into recipient cell.
GENE MAPPING IN PHAGES
Mapping genes in the bacteriophages themselves depends on homolgous
recombination between phage chromosomes.
Crosses are made between viruses that differ in two or more genes, and
recombinant progeny phages are identified and counted.
PURPOSE: The proportion of recombinant progeny is then used to
estimate the distances between the genes and their linear order on the
chromosome.
EXPERIMENT:In 1949, ALFRED HERSHEY and RAQUEL
ROTMAN examined rates of recombination in the T2 bacteriophage, which
has single-stranded DNA.

16.  They studied recombination between genes in two strains that differed in
plaque appearance and host range (the bacterial strains that the phages
could infect).
 One strain was able to infect and lyse type B E. coli cells but not type
B/2 E. coli cells (making this strain of bacteria wild type with normal
host range, or h+) and produced an abnormal plaque that was large with
distinct borders (r−).
 The other strain was able to infect and lyse both B and B/2 cells (mutant
host range, h−) and produced wild-type plaques that were small with
fuzzy borders (r+).
 Hershey and Rotman crossed the h+ r− and h− r+ strains of T2 by
infecting type B E. coli cells with a mixture of the two strains.
 They used a high concentration of phages so that most cells could be
simultaneously infected by both strains.
 Within the bacteria cells, homologous
 recombination occasionally took place between the chromosomes
 of the different bacteriophage strains, producing h+ r+ and h− r−
chromosomes, which were then packaged into new phage particles.
 When the cells lysed, the recombinant phages were released, along with
the nonrecombinant h+ r− phages and h− r+ phages.
 Hershey and Rotman diluted and plated the progeny phages on a
bacterial lawn that consisted of a mixture of B and B/2 cells. Phages
carrying the h+ allele (which conferred the ability to infect only B cells)
produced a cloudy plaque because the B/2 cells did not lyse. Phages
carrying the h− allele produced a clear plaque because all the cells
within the plaque were lysed. The r+ phages produced small plaques,
whereas the r− phages produced large plaques.
 The genotypes of these progeny phages could therefore be determined
by the appearance of the plaque.

17. CALCULATION: In this type of phage cross, the recombination
frequency (RF) between the two genes can be calculated by using the
following formula:
In Hershey and Rotman’s cross, the recombinant plaques were h+ r+ and h−
r− so the recombination frequency was
RESULT: Recombination frequencies can be used to determine the
distances between genes and their order on the phage chromosome.

19. FINE STRUCTURE ANALYSIS OF BACTERIOPHAGE
GENE
In the 1950s and 1960s, SEYMOUR BENZER conducted a series of
experiments to examine the structure of a gene. Because no molecular
techniques were available at the time for directly examining nucleotide
sequences, Benzer was forced to infer gene structure from analyses of
mutations and their effects.
The results of his studies showed that different
mutational sites within a single gene could be mapped (referred to as
intragenic mapping) by using techniques similar to those described for
mapping bacterial genes by transduction.
Because large numbers of progeny are required to detect these recombination
events, Benzer used the bacteriophage T4, which reproduces rapidly and
produces large numbers of progeny.
Benzer’s mapping techniques
Wild-type T4 phages normally produce small plaques with rough edges when
grown on a lawn of E. coli. Certain mutants, called r for rapid lysis, produce
larger plaques with sharply defined edges.
METHOD-
 Benzer isolated phages with a number of different r mutations,
concentrating on one particular subgroup called rII mutants.
 Wild-type T4 phages produce typical plaques on E. coli strains B and K.
In contrast, the rII mutants produce r plaques on strain B and do not
form plaques at all on strain K.
 Benzer recognized the r mutants by their distinctive plaques when
grown on E. coli B.
 He then collected lysate from these plaques and used it to infect E. coli
K. Phages that did not produce plaques on E. coli K were defined as the
rII type.
 Benzer collected thousands of rII mutations.

20.  He simultaneously infected bacterial cells with two different mutants
and looked for recombinant progeny
 Consider two rII mutations, a− and b− (their wild-type alleles are a+ and
b+).
 Benzer infected E. coli B cells with two different strains of phages, one
a− b+ and the other a+ b− (step 3).
 Neither of these mutations is able to grow on E. coli K cells.
 While reproducing within the B cells, a few phages of the two strains
recombined (step 4).
OBSERVATION: A single crossover produces two recombinant
chromosomes; one with genotype a+ b+ and the other with genotype a− b−:
 The resulting recombinant chromosomes, along with the non-
recombinant (parental) chromosomes, were incorporated into progeny
phages, which were then used to infect E.coli K cells.
 The resulting plaques were examined to determine the genotype of the
infecting phage and map the rII mutants (step 5).
 Neither of the rII mutants grew on E. coli K (step 2), but wild-type
phages grew; so progeny phages that produced plaques on E. coli K
must have the recombinant genotype a+ b+.
 Each recombination event produces equal numbers of double mutants
(a− b−) and wild-type chromosomes (a+ b+).
 Therefore, the number of recombinant progeny should be twice the
number of wild-type plaques that appeared on E. coli K.

21. CALCULATION: The recombination frequency between the two rII
mutants would be:
RESULT: Because phages produce large numbers of progeny, Benzer was
able to detect a single recombinant among billions of progeny phages.
Recombination frequencies are proportional to physical distances along the
chromosome, revealing the positions of the different mutations within the rII
region of the phage chromosome.
In this way, Benzer eventually mapped more than
2400 rII mutations, many corresponding to single base pairs in the viral DNA.
His work provided the first molecular view of a gene.

22. RNA VIRUS AND RETROVIRUS
 Viral genomes may be encoded in either DNA or RNA, as stated earlier.
 RNA is the genetic material of some medically important human viruses,
including those that cause influenza, common colds, polio, and AIDS.
Almost all viruses that infect plants have RNA genomes.
 The medical and economic importance of RNA viruses has encouraged
their study.
 RNA viruses capable of integrating into the genomes of their hosts,
much as temperate phages insert themselves into bacterial chromosomes,
are called retroviruses.
 Because the retroviral genome is RNA, whereas that of the host is DNA,
a retrovirus must produce reverse transcriptase, an enzyme that
synthesizes complementary DNA (cDNA) from either an RNA or a
DNA template.
 A retrovirus uses reverse transcriptase to copy its RNA genome into a
single-stranded DNA molecule, which it then copies to make double-
stranded DNA. The DNA copy of the viral genome then integrates into
the host chromosome. A viral genome incorporated into the host
chromosome is called a provirus.
 The provirus is replicated by host enzymes when the host chromosome
is duplicated.
 When conditions are appropriate, the provirus undergoes transcription to
produce numerous copies of the original viral RNA genome.
 This RNA encodes viral proteins and serves as genomic RNA for new
viral particles.
 As these viruses escape the cell, they collect patches of the cell
membrane to use as their envelopes.
 All known retroviral genomes have in common three genes:
1. gag (encodes proteins that make up the viral protein coat),
2. pol (encodes reverse transcriptase and an enzyme called integrase
that inserts the viral DNA into the host chromosome), and
3. env (gene encodes the glycoproteins that appear on the surface of
the virus), each encoding a precursor protein that is cleaved into
two or more functional proteins.
Some retroviruses contain oncogenes that may stimulate cell division and
cause the formation of tumors.

24. OTHER VIRUSES AND DISEASE CAUSED
BY THEM:
DISEASE PATHOGEN SYMPTOMS DIAGRAM
Hepatitis
Hepatitis
A,B,C,D,E
fever, fatigue, loss
of appetite, nausea,
vomiting, abdomina
l pain, dark urine,
light-colored
stools, joint pain,
and jaundice
Influenza Influenza virus
fever, chills, muscle
aches, cough,
congestion,runny
nose, headaches
and fatigue

25. DISEASE PATHOGEN SYMPTOMS DIAGRAM
AIDS
Human
immunodeficiency
virus (HIV)
weight loss, fever
or night sweats,
fatigue and
recurrent
infections
Measles Measles virus
high fever, soar
throat, mascular
rash, spots on
oral mucosa, etc
Chicken
pox
Varicella zoster
virus
In childern; fever,
chills, rash of
lesions that
bursts and form
crushy scrabs. In
adults; more
severe symptoms
and
complications
such as
pneumonia.
MERS
Middle east
respiratory
syndrome
coronavirus
(MERS-Co)
fever, cough,
shortness of
breath, and other
complications
SARS
SARS associated
coronavirus
high fever,
headache, body
ache, dry cough,
pneumonia, etc.

26. LATEST STUDIES
(A) HEPATITIS C VIRUS:
Hepatitis C is a contagious liver infection caused by the hepatitis C virus
(HCV). The hepatitis C virus was discovered in 1989 by Harvey J.
Alter, Michael Houghton and Charles M. Rice.
HIGHLIGHT:
The 2020 Nobel Prize in Physiology or Medicine is awarded to Harvey J.
Alter, Michael Houghton and Charles M. Rice for the discovery of Hepatitis
C virus.
SYMPTOMS:
Hepatitis, from the Greek names for liver and inflammation, is a disease
characterized by poor appetite, vomiting, fatigue and jaundice – yellow
discoloration of the skin and eyes. Chronic hepatitis leads to liver damage,
which may progress to cirrhosis and liver cancer.
FACTS:
Globally, an estimated 71 million people have chronic hepatitis C virus
infection.
A significant number of those who are chronically infected will develop
cirrhosis or liver cancer.
WHO estimated that in 2016, approximately 3,99, 000 people died from
hepatitis C, mostly from cirrhosis and hepatocellular carcinoma (primary liver
cancer).
FOR FUTHER DETAILS:
https://www.nobelprize.org/prizes/medicine/2020/advanced-information/
https://www.who.int/news-room/fact-sheets/detail/hepatitis-c

27. DIAGRAM: HEPATITIS C VIRUS

28. (B) CORONAVIRUS
Coronaviruses are a large family of viruses that are known to cause illness
ranging from the common cold to more severe diseases such as Middle East
Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome
(SARS).
FIRST DISCOVER:
JUNE ALMEIDA was the first woman who discovered the first human
coronavirus in the year 1964 at her laboratory in St Thomas's Hospital in
London.
NAMING:
The International Committee on Taxonomy of Viruses (ICTV) announced
“severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” as the
name of the new virus on 11 February 2020. This name was chosen because
the virus is genetically related to the corona virus responsible for the SARS
outbreak of 2003.
ORIGIN:
The first human cases of COVID-19, the disease caused by the novel
coronavirus, subsequently named SARS-CoV-2 were first reported by
officials in Wuhan City, China, in December 2019.
SYMPTOMS:
Shortness of breath, A cough that gets more severe over time, A low-
grade fever that gradually increases in temperature, Chills, fatigue, repeated
shaking with chills, sore throat, headache, muscle aches and pains, loss of
taste or smell, a stuffy or runny nose, gastrointestinal symptoms such as
diarrhea, nausea, and vomiting, discoloration of fingers or toes, pink eye and
rash.
FACTS:

29. The coronavirus outbreak (COVID-19) is confirmed as pandemic by WHO,
11 march,2020.
The virus that causes COVID-19 is mainly transmitted through droplets
generated when an infected person coughs, sneezes, or exhales,or by touching
a contaminated surface and then your eyes, nose or mouth.
It consists of the proteins in the outer membrane, known as spike proteins (S).
It is these proteins which are recognized by receptor proteins on the host cells
which will be infected.
DIAGRAM: CORONA VIRUS
REFERENCE
GENETICS A CONCEPTUAL APPROACH: BENJAMIN A. PIERCE- 4th
Edition
https://www.nobelprize.org/prizes/medicine/2020/advanced-
information/
https://www.who.int/news-room/fact-sheets/detail/hepatitis-c