A comprehensive illustration about viruses and their genetic system. 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.

1. SONAL SINGH SHRIVAS

2. 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 structure analysis if bacteriophage gene
 Benzer’s mapping techniques
2. RNA and retrovirus
3. Animal virus
4. Plant virus
 Other viruses and disease caused by them
 Latest studies
 Reference:

3. 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. 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.

4. 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 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.”

5. 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.

6.  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.
 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
 those lacking an envelope are called naked viruses (or non-enveloped
viruses).

7.  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.

8. SHAPE AND SIZE
SIZE:
Viruses are smaller than prokaryotic cells (such as bacteria) ranging in size from 0.02-
0.3 mm.
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:
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.

9. 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.
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.

10. 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

11.  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.

13. 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.
T4 is an example of complex phage.

14. 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:
i. Lytic cycle
ii. Lysogenic cycle

16.  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.
 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.

17. Plaques are clear patches of lysed cells on a lawn of bacteria.

18. 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
2) SPECIALIZED TRANSDUCTION

19. GENERALIZED TRANSDUCTION

20. 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.

21. SPECIALIZED TRANSDUCTION:

22.  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 gene are
situated on the side of integrated viral genome have a chance to enter into
recipient cell.

23. 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.

24. 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+).
h+ wild type bacteria with
normal host range
h− mutant host range
r+ wild-type plaques +
small with fuzzy borders
r− abnormal plaque + large
with distinct borders

26. 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.

27. 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.

28. 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.
 He simultaneously infected bacterial cells with two different
mutants and looked for recombinant progeny

30. 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+).

31. 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.

32.  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.
 All known retroviral genomes have in common three genes:
• gag (encodes proteins that make up the viral protein coat),
• pol (encodes reverse transcriptase and an enzyme called integrase that inserts
the viral DNA into the host chromosome), and
• 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.

36. 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.

37. 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

38. CORONA VIRUS
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.

39. 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, soar throat, headache, muscle ache and pain,
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:
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.

40. 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