Module 9 Viral Genome and Diversity

General Microbiology
Module 9:
Viral Genomes and Diversity
(Week 13 & 14)
by:
ARCIBEL B. BAUTISTA, M.A.T - Science
OVERVIEW:
• Viruses are too small to be seen with light microscope
and cannot be cultured outside their hosts.
• Viruses are found as parasites in all types of organisms.
Although viruses must live inside a host cell, not all of
them cause a disease.
LEARNING OUTCOMES:
After successful completion of this module, the learner should be
able to:
1. identify the different structural components of virion
2. categorize the characteristics of viral genome;
3. discuss the viral growth curve
Read: Tortora, G. et.al. Microbiology: An Introduction. (2013) 11th
ed. Pearson Educ. Inc. p. 379.
Course Material:
I. Nature of Virus
Virus – obligate intracellular parasite
Virion
- complete, fully developed, infectious viral particle
- composed of nucleic acid and surrounded by a protein
coat.
- most viruses are smaller than prokaryotic cells
- 0.02 to 0.3 μm (20–300 nanometers, nm)
Viral Structure
Course Material:
Components of Virion Structure:
1. Nucleic Acid – always surrounded by capsid (either DNA or RNA)
2. Capsid – nucleic acid surrounded by capsomere ( individual protein
coat or molecules)
Nucleocapsid - a unit of viral structure, consisting of a capsid with the
enclosed nucleic acid.
Envelope- one that covers the capsid

Non-enveloped or naked virus - those not covered
- composed of combination of lipid, protein and carbohydrates.
- may or may not be covered by spikes
Read: Tortora, G. et.al. Microbiology: An Introduction.
(2013) 11th ed. Pearson Educ. Inc., p. 379.
Enveloped viruses
Influenza virus – 80 nm in diameter and Vaccinia virus – enveloped icosahedral
can have many shapes pox virus. 350 nm in wide
Course Material:
Enveloped Viruses – roughly spherical.
enveloped helical virus - helical virus enclosed with an
envelope
e.g. Influenza virus
enveloped polyhedral virus – polyhedral virus enclosed
with an envelope
e.g. Herpes simplex virus
(2013) 11th ed. Pearson Educ. Inc. pp. 380-381.
Course Material:
I. Viral Symmetry
1. Helical Viruses – long rods that may be rigid or flexible.
The nucleic acid is found within hollow, cylindrical capsid
that has a helical structure.
e.g. Rabies, Ebola, Tobacco Mosaic Virus (TMV)
Read: Madigan, M.T. et.al.. Brock Biology of

Microorganisms 15th ed. (2019) Pearson Educ.
Inc. p.261.
The RNA forms a helix
surrounded by a protein
sub-units (capsomeres).
The center of the virus
particle is hollow
Course Material:
2. Icosahedral Viruses –
animal, plant and bacterial
viruses are polyhedral.
- The capsid is in the shape
of icosahedron (20 triangular
faces and 12 corners).
- Capsomeres are
equilateral triangle.
e.g. Adenovirus, Poliovirus,
Picornavirus, Papovavirus,
Herpes
(2013) 11th ed. Pearson Educ. Inc. pp. 380-381.
Course Material:
3. Complex viruses – being composed of several separate
capsomere with separate shape and symmetry
e.g. bacteriophage, Pox virus
Read: Madigan, M. T. et.al.. Brock Biology of
Microorganisms 15th ed. (2019). Pearson, Educ. Inc. p. 260.
Course Material:
II. Viral Genome
- consist either DNA or RNA
- single or double stranded
- can either be linear or circular
Base sequence:
- the single stranded genome + sense or – sense
- The plus (+) configuration have the exact same base sequence
as that of the viral mRNA that will be translated to form viral
proteins.
- The minus (-) configuration are complementary in base
sequence to viral mRNA.
Course Material:
Characteristics of Viral Genome
1. Living characteristics of 2. Non-living characteristics of
viruses viruses
a. They reproduce at a a. They are acellular, that is,
they contain no cytoplasm or
fantastic rate, but only in cellular organelles.
living host cells.
b. They carry out no metabolism
b. They can mutate. on their own and must replicate
using the host cell's metabolic
machinery.
c. either DNA or RNA
Read: Madigan, M.T. et.al.. Brock Biology of Microorganisms 15th ed.
(2019) Pearson Educ. Inc. pp. 315-319.
Course Material:
Viruses with DNA Genome
1. Bacteriophage fX174
- contains a circular genome of 5386 nucleotides inside a tiny icosahedral virion,
about 25 nm in diameter.
- Phage fX174 has only a few genes and shows the phenomenon of overlapping
genes, a condition in which there is insufficient DNA to encode all viral-specific
proteins unless parts of the genome are read more than once in different reading
frames.
2. Bacteriophage M13
- Filamentous virus with helical symmetry; the virion is long and thin and attaches
to the pilus of its host cell.
- Filamentous phages such as M13 have the unusual property of being released
from the host cell without the cell undergoing lysis; infected cells continue to
grow, and typical viral plaques are not observed.
Course Material:
Double stranded DNA Bacteriophages
1. Bacteriophage T7 is a relatively small DNA virus that infects
Escherichia coli and a few related enteric bacteria. The virion
has an icosahedral head and a very short tail, and the T7
genome is a linear double-stranded DNA molecule of about 40
kilobase pairs.
2. Bacteriophage Mu is an icosahedral head, a helical tail, and
several tail fibers. The genome of Mu consists of linear
double-stranded DNA, and most Mu genes encode head and
tail proteins, other replication factors such as the Mu
transposase, and factors that affect host range.
Course Material:
Viruses with RNA Genome
1. Positive strand RNA Viruses
e.g. Polio, Rhinovirus, Coronavirus, SARS, Hepatitis A
a. Bacteriophage MS2
Bacteriophage MS2 is about 25 nm in diameter and has an icosahedral
capsid. The virus infects cells of Escherichia coli by attaching to the
cell’s pilus, a structure that normally functions in a form of horizontal
gene exchange (conjugation) in bacteria.
A 3.5 kb in size and encodes only four proteins, including the
maturation protein, coat protein, lysis protein, and one subunit of
RNA replicase, the enzyme that replicates the viral RNA.
Course Material:
2. Negative strand RNA Animal Viruses
- the genomes of these negative-strand RNA viruses are
complementary in base sequence to the mRNA that is formed.
- examples of negative strand RNA viruses: Rabies virus and
Influenza virus.
- There are no known negative-strand RNA bacteriophages or
Archaeal viruses.
3. Double stranded RNA Viruses
- Viruses with double-stranded RNA genomes. Reoviruses are an
important family of animal viruses.
- e.g. Reovirus --- Rotavirus
Course Material:
4. Viruses that Uses Reverse Transcriptase
- Two different classes of viruses use reverse transcriptase, and
they differ in the type of nucleic acid in their genomes;
- Retroviruses have RNA genomes while Hepadnaviruses have
DNA genomes (Baltimore classes VI and VII, respectively).
- Besides their unique molecular properties, both classes of
viruses include important human pathogens, including HIV (a
retrovirus) and Hepatitis B (a hepadnavirus).
Course Material:
Baltimore Classes of Viruses
Class I – Double stranded DNA (dsDNA) Viruses
A double stranded DNA virus enters the host nucleus before it begins to replicate.
It makes use of the host polymerases to replicate its genome, and is therefore highly
dependent on the host cell cycle. The cell must therefore be in replication for the
virus to replicate.
Examples of Class I viruses include Herpesviridae, Adenoviridae, and Papoviridae.
Class II: Single stranded DNA (ssDNA) viruses
Most ssDNA viruses have circular genomes and replicate mostly within the nucleus
by a rolling circle mechanism.
Examples of Class II viruses are Anelloviridae, Circoviridae, and Parvoviridae.
https://www.news-medical.net/life-sciences/The-Baltimore-Classification-System.aspx
Course Material:
Class III: Double stranded RNA (dsRNA) viruses
Double stranded RNA viruses replicate in the core capsid in the host cell
cytoplasm and do depend as heavily on host polymerases as DNA viruses.
The genomes of Class III viruses may be segmented, and unlike viruses with
more complex translation, each gene codes for only one protein.
Examples of Class III viruses include Rheoviridae and Birnaviridae.
Class IV: Single stranded RNA (ssRNA) viruses
Class IV ssRNA viruses have positive-sense RNA genomes, meaning they
can be directly read by ribosomes to translate into proteins. They are further
divided into viruses with polycistronic mRNA and those with complex
transcription.
Examples of some Class IV viruses
are Coronaviridae, Flaviviridae, Astroviridae, and Picornaviridae.
Course Material:
Class V: Single stranded RNA (ssRNA) viruses
Class V viruses have a negative-sense RNA genome, meaning they must be
transcribed by a viral polymerase to produce a readable strand of mRNA.
The genomes of Class V viruses may be segmented or non-segmented.
Some viruses in Class V are Orthomyxoviridae, Paramyxoviridae,
and Rhabdoviridae.
Class VI: Positive-sense ssRNA reverse transcriptase viruses
Group VI viruses have a positive sense, single-stranded RNA genome, but
replicate through a DNA intermediate. The RNA is converted to DNA by
reverse transcriptase and then the DNA is spliced into the host genome for
subsequent transcription and translation using the enzyme integrase.
Group VI includes Retroviruses such as HIV, as well
as Metaviridae and Pseudoviridae.
Course Material:
Class VII: Double stranded DNA (dsDNA) reverse
transcriptase viruses
Class VII viruses have a double-stranded DNA genome, but
unlike Class I viruses, they replicate via a ssRNA intermediate.
The dsDNA genome is gapped, and subsequently filled in to
form a closed circle serving as a template for production of viral
mRNA. To reproduce the genome, RNA is reverse transcribed
back to DNA. Hepatitis B virus is a Class VII virus.
Read: Tortora, G. et.al. Microbiology: An Introduction. (2013) 11th ed.
Pearson Educ. Inc. Pearson Educ. Inc. p. 381.
Course Material:
III. Taxonomy of Viruses:
- International Committee on the Taxonomy of Viruses (ICTV) has been
grouping the viruses into families based on:
1. Nucleic acid type 2. Strategy for replication 3. morphology
- The suffixes:
Order names end in –ales.
Family names end in –viridae;
Genus names -virus;
- Viral species is a group of viruses sharing the same genetic information
and ecological niche. Specific epithets for viruses are not used.
e.g. HIV, with subspecies designated by a number HIV-1
Course Material:
Isolation, Cultivation and Identification of Viruses
- Viruses cannot multiply outside a living host cell complicates their
detection, enumeration, and identification .
- Viruses must be provided with living cells instead of a fairly simple
chemical medium.
- Living plants and animals are difficult and expensive to maintain.
- Pathogenic viruses that grow only in higher primates and human
host can cause additional complications.
- Bacteriophage easily grown on bacterial cultures.
- Viral multiplication has come from bacteriophage.
Read: Tortora, G. et.al. Microbiology: An Introduction. (2013) 11th ed. Pearson Educ.
Inc. p. 381.
Course Material:
Viral Identification
1. Western Blotting – the serological test that is commonly
used in identifying viruses
2. Restriction Fragment Length Polymorphisms (RFLP)
3. Polymerase Chain Reaction (PCR)
Read: Tortora, G. et.al. Microbiology: An Introduction. (2013) 11th ed. Pearson Educ. Inc. p. 386.
Course Material:
IV. Viral Replication
- Viruses do not contain enzymes
for energy production of protein
synthesis
- For a virus to multiply, it must
invade a host cell and direct the
host’s metabolic machinery to
produce vital enzymes and
components
Read: Madigan, M.T. et.al.. Brock Biology of Microorganisms 15th ed. (2019) Pearson
Educ. Inc. p. 264
Course Material:
Bacteriophage
-viruses that infect
bacteria
obligate intracellular
pathogens
they must enter the
bacterial cell to
replicate
Course Material:
2 Primary Types of Bacteriophage
A. Virulent phages – also B. Temperate phages - known as
known as the LYTIC CYCLE the LYSOGENIC CYCLE,
Bacteriophages that replicate Do not immediately initiate the
through the lytic life cycle are lytic cycle, but rather, their DNA
called lytic bacteriophages, remains integrated into the
and are so named because they bacterial cell chromosomes,
lyse the host bacterium as a generation after generation, and
normal part of their life cycle, become a noninfectious
which ends with the prophage.
destruction (lysis) of the
bacterial cell.
Course Material:
Growing of Bacteriophage Growing of Animal Viruses
- grown either in suspension of Methods used in culturing
bacteria in liquid media or animal viruses
bacterial cultures of solid a. Living animals
media.
b. Embryonated eggs
Plaque Assay method –
used for detecting viruses in c. Cell cultures
solid media
Inc. p. 384.
Course Material:
V. Viral Infection – a process where the viruses cannot replicate or
reproduce unless the virion itself (or its genome, in the case of bacterial
viruses) has gained entry into a suitable growing host cell.
Virulent Lytic Infection

• The virus may replicate and destroy the host
• In a lytic infection, the virus redirects the host cell’s metabolism from
growth to support virus replication and the assembly of new virions.
• new virions are released, and the process can repeat itself with new host
cells.
Read: Madigan, M.T. et.al.. Brock Biology of Microorganisms
15th ed. (2019) Pearson Educ. Inc. pp.263-264.
Course Material:
Virus Lytic Cycle
1. Attachment (adsorption) of the virion to the host cell
2. Penetration (entry, injection) of the virion nucleic acid into the
host cell
3. Synthesis of virus nucleic acid and protein by host cell
machinery as redirected by the virus
4. Assembly of capsids and packaging of viral genomes into
new virions
5. Release of new virions from the cell
Lytic Cycle
https://www.researchgate.net/publication/343167119_An_exegesis_of_bacteriophage_therapy_An_emergi
ng_player_in_the_fight_against_anti-microbial_resistance/figures?lo=1
Lysogenic Cycle of Bacteriophage λ in E. coli
Inc. p. 389.
Basic differences between the lytic and lysogenic
cycles of a viral infection are
• In lytic cycle, the viral DNA destroys cell DNA, takes over cell
functions and destroys the cell.
• In lysogenic cycle, the viral DNA merges with cell DNA and
does not destroy cell.
• In lytic cycle, the virus replicates and produces progeny phages.
• In lysogenic cycle, the virus does not produce progeny.
Basic differences between the lytic and lysogenic
cycles of a viral infection are
• In lytic cycle, there are symptoms of viral infection.
• In lysogenic cycle, there are no symptoms of viral infection.
• Virulent viral replication takes place by lytic cycle.

• Temperate viral replication takes place by lysogenic cycle.
Course Material:
Viruses and Cancer
- Several types of cancer are now known to be caused by viruses.
- Molecular biological research shows that the mechanisms of the
disease are similar, even when a virus does not cause the cancer.
- The viral cause of cancer can often go unrecognized for several
reasons.
- First, most of the particles of some viruses infect cells but do
not induce cancer.
- Second, might not develop until long after viral infection.
- Third, cancers do not seem to be contagious, as viral diseases
usually are.
Inc. p. 399.
Course Material:
Latent Viral Infection
- virus remain in the host cell for long periods without producing
the infection.
e.g. cold sores, shingles
Persistent Viral Infection
-disease processes that occur over a long period and generally are
fatal.
-caused by conventional viruses; viruses that accumulate over a
long period.
Inc. p. 401.
(2013) 11th ed. Pearson Educ. Inc. pp. 401-403
Course Material:
Sub-viral Agents
Prions
- Prions are infectious proteins
- Disease such as Creutzfeldt Jakob Disease (CJD) and mad cow disease are involve
in the degeneration of brain tissue.
- Prion disease are the result of an altered protein.
Plant Viruses
- Must enter plant hosts through wounds or with invasive parasites such as insects.
- Some plant viruses also multiply in insect cells.
Viroids
- Infectious pieces of RNA that cause some plant diseases such as potato spindle
tuber viroid disease.
Activities/Assessments:
In a separate sheet of paper, write the name, section, module number, title
and questions. Then briefly discuss the following questions:
1. Why does viruses are considered as obligate intracellular parasites?

(10 points)
2. Draw and explain the growth curve of virus replication (10 points)
3. Differentiate the following:
a. lytic from lysogenic cycle (10 points)
b. latent from persistent viral infection (10 points)
4. Discuss what happened to the brain tissue of a cow infected with prions.
(10 points)
Grading System:
Each question is equivalent to 10 points per number
RUBRICS FOR SCORING ESSAY QUESTION

5 4 3 2 1
The student has full The student has a good The student has a basic The student has some The student has no
Level of Understanding understanding of the understanding of the understanding of the understanding of the understanding of
question or problem question or problem question or problem question or problem the question or
The response reflects a The response reflects The response provides problem. The
The response addresses
Synthesis of Information complete synthesis of some synthesis of little or no synthesis of response is
the question
information information information completely
Total Score = _________ / 10 x 100 = _________%

Reference:
As a reading material, you will be needing a book or an e-book:
• Madigan, M.T.. Brock Biology of Microorganisms (2019) 15th ed.

Pearson Educ. Inc.
• Tortora, G. et al.. Microbiology: An Introduction (2013) 11th ed.
Pearson Educ. Inc.

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General Microbiology

Envelope- one that covers the capsid

Read: Madigan, M.T. et.al.. Brock Biology of

Virulent Lytic Infection

• Virulent viral replication takes place by lytic cycle.

1. Why does viruses are considered as obligate intracellular parasites?

RUBRICS FOR SCORING ESSAY QUESTION

Total Score = _ / 10 x 100 = _%

• Madigan, M.T.. Brock Biology of Microorganisms (2019) 15th ed.

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