Uploaded by Asma Ayad Ghazi

Lec 4 Viral Genetics

Spring 2022
Microbiology II course
Virology- Week 4 (Viral Genetics)
Assist. Prof. Dr. Dana Khdr Sabir
2021- 2022
Learning outcome
1- Basic revision of molecular genetics
2- Viral classification
3- Viral variations
PART 1: What is Genetics?
• Genetics is a branch of biology concerned with the study of
genes, genetic variation, and heredity in organisms
The central dogma of
molecular biology
explains the flow of
genetic information,
from DNA to RNA, to
make a functional
product, a protein.
Central Dogma of Molecular Biology
Full Name
Deoxyribonucleic Acid
Ribonucleic Acid
DNA replicates and stores genetic
information. It is a blueprint for all genetic
information contained within an organism.
RNA converts the genetic information
contained within DNA to a format used
to build proteins, and then moves it to
ribosomal protein factories.
DNA consists of two strands, arranged in a
double helix. These strands are made up of RNA only has one strand, but like DNA, is
subunits called nucleotides. Each nucleotide made up of nucleotides. RNA strands are
contains a phosphate, a 5-carbon sugar
shorter than DNA strands.
molecule and a nitrogenous base.
DNA is a much longer polymer than RNA.
The sugar in DNA is deoxyribose, which
contains one less hydroxyl group than RNA’s
RNA molecules are variable in length,
but much shorter than long DNA
RNA contains ribose sugar molecules,
without the hydroxyl modifications of
The bases in DNA are
Adenine (‘A’), Thymine (‘T’), Guanine (‘G’)
and Cytosine (‘C’).
RNA shares Adenine (‘A’), Guanine
(‘G’) and Cytosine (‘C’) with DNA, but
contains Uracil (‘U’) rather than
Thymine (T).
Adenine and Thymine pair (A-T)
Cytosine and Guanine pair (C-G)
Adenine and Uracil pair (A-U)
Cytosine and Guanine pair (C-G)
DNA is found in the nucleus, with a small
amount of DNA also present in
RNA forms in the nucleolus, and then
moves to specialised regions of the
cytoplasm depending on the type of
RNA formed.
Due to its deoxyribose sugar, which contains
one less oxygen-containing hydroxyl group,
DNA is a more stable molecule than RNA,
which is useful for a molecule which has the
task of keeping genetic information safe.
RNA, containing a ribose sugar, is
more reactive than DNA and is not
stable in alkaline conditions. RNA’s
larger helical grooves mean it is more
easily subject to attack by enzymes.
Ultraviolet (UV)
DNA is vulnerable to damage by ultraviolet RNA is more resistant to damage
from UV light than DNA.
Base Pairs
Main differences between DNA, RNA
The Genetic Code: Codons
• The genetic code is read in
three- letter grouping called
• A codon is a group of three
nucleotide bases in messenger
RNA that specifies a particular
amino acids.
PART 2: Viral Classification
• Taxonomy is the science of
categorizing and assigning
names (nomenclature) to
organisms based on similar
• It is important to note that
viruses, since they are not alive,
belong to a completely separate
system that does not fall under
the tree of life (Phylogenetic
Virus Classification and Taxonomy
Why classification?
1. It allows scientists to contrast viruses and to reveal information on
newly discovered viruses by comparing them to similar viruses.
2. It also allows scientists to study the origin of viruses and how they have
evolved over time.
The classification of viruses is not simple, however—there are currently
over 2800 different viral species with very different properties!
Viral Classification
• Since viruses lack ribosomes (and thus rRNA), they cannot be
classified within the Three Domain Classification scheme with cellular
• Dr. David Baltimore derived a viral classification scheme, one that
focuses on the relationship between a viral genome to how it produces
its mRNA.
• The Baltimore Scheme recognizes seven classes of viruses.
Viruses are only classified using order, family,
genus, and species
Order: Ends in virales suffix (such as
Family: Ends in- viridae suffix, subfamilies
are indicated with virinae suffix Such as
Genus: Ends in –virus suffix. Such as
Species: Generally the common names of
the virus.
Virus Classification and Taxonomy
The Baltimore classification system:
• This system categorizes viruses based on the type of nucleic acid
genome and replication strategy of the virus. The system also breaks
down single-stranded RNA viruses into those that are positive strand (+)
and negative strand (−).
• Positive-strand (also positive-sense or plus-strand) RNA is able to be
immediately translated into proteins; as such, messenger RNA (mRNA)
in the cell is positive strand.
Virus Classification and Taxonomy
• Negative-strand (also negative-sense or minusstrand) RNA is not
translatable into proteins; it first has to be transcribed into positive-strand
• Baltimore also took into account viruses that are able to reverse
transcribe, or create DNA from an RNA template, which is something
that cells are not capable of doing.
Seven viral classes:
• Class I: dsDNA viruses
• Class II: ssDNA viruses
• Class III: dsRNA viruses
• Class IV: positive-sense (+) ssRNA viruses
• Class V: negative-sense (-) ssRNA viruses
• Class VI: RNA viruses that reverse transcribe
• Class VII: DNA viruses that reverse transcribe
DNA viruses (Class I, II, and VII)
Class I: dsDNA
• DNA viruses with a dsDNA genome have a genome exactly the same as the host cell that
they are infecting. Therefore, many host enzymes can be utilized for replication and/or protein
• The flow of information follows a conventional pathway: dsDNA → m R N A → protein.
• DNA-dependent RNA-polymerase producing the mRNA and the host ribosome producing
the protein.
• The genome replication, dsDNA → dsDNA, requires a DNA-dependent DNApolymerase from either the virus or the host cell.
Example like: bacteriophages T4 and lambda
DNA viruses (Class I, II, and VII)
• Class II: ssDNA
• ssDNA viruses can either have the same base sequence as the mRNA (plus-strand
DNA) or be complementary to the mRNA (minus-strand DNA).
• For the plus-strand DNA viruses, the complementary to the viral genome must be
manufactured first, forming a double-stranded replicative form (RF). This can be
used to both manufacture viral proteins and as a template for viral genome copies.
• For the minus-strand DNA viruses, the genome can be used directly to produce
mRNA but a complementary copy will still need to be made, to serve as a template
for viral genome copies.
Example: Parvoviruses
Class II
DNA viruses (Class I, II, and VII)
• Class VII: DNA viruses that use reverse transcriptase
• The viruses of this class has a DNA genome that is partially double-stranded,
but contains a single-stranded region.
• After gaining entrance into the cell’s nucleus, host cell enzymes are used to fill
in the gap with complementary bases to form a dsDNA closed loop
• Gene transcription yields a plus-strand RNA known as the pregenome, as well
as the viral enzyme reverse transcriptase, an RNA-dependent DNApolymerase.
• The pregenome is used as a template for the reverse transcriptase to
produced minus-strand DNA genomes, with a small piece of pregenome used
as a primer to produce the double-stranded region of the genomes.
Example: Hepadnaviruses
Reverse transcriptase
RNA viruses (Class III, IV, V, VI)
• RNA Genome strategies
• RdRp: virus encoded for RNA dependent RNA polymerase
• RT: Virus encoded Reverse Transcriptase
RNA viruses (Class III, IV, V, VI)
Class III: dsRNA
• Double-stranded RNA viruses infect bacteria, fungi, plants, and animals, such as the
rotavirus that causes diarrheal illness in humans.
• Cells do not utilize dsRNA in any of their processes and have systems in place to
destroy any dsRNA found in the cell. Thus the viral genome, in its dsRNA form, must
be hidden or protected from the cell enzymes.
• Cells also lack RNA-dependent RNA-polymerases, necessary for replication of the
viral genome so the virus must provide this enzyme itself. The viral RNA-dependent
RNA polymerase acts as both a transcriptase to transcribe mRNA, as well as
a replicase to replicate the RNA genome.
Class III: dsRNA (Continue..)
• Messenger RNA is transcribed from the
minus-strand of the RNA genome and then
translated by the host ribosome in the
• Viral proteins aggregate to form new
nucleocapsids around RNA replicase and
plus-strand RNA.
• The minus-strand RNA is then synthesized
by the RNA replicase within the
nucleocapsid, once again insuring
protection of the dsRNA genome.
RNA viruses (Class III, IV, V, VI)
• Class IV: +ssRNA
• Viruses with plus-strand RNA can use their genome directly as
mRNA with translation by the host ribosome occurring as soon as
the unsegmented viral genome gains entry into the cell.
• One of the viral genes expressed yields an RNA-dependent RNApolymerase (or RNA replicase), which creates minus-strand RNA
from the plus-strand genome.
• The minus-strand RNA can be used as a template for more plusstrand RNA, which can be used as mRNA or as genomes for the
newly forming viruses.
such as coronoviridae, poliovirus
Class IV: +ssRNA
RNA viruses (Class III, IV, V, VI)
• Class V: -ssRNA
• Minus-strand RNA viruses include many members notable for humans,
such as influenza virus, rabies virus, and Ebola virus.
• Since the genome of minus-strand RNA viruses cannot be used directly as
mRNA, the virus must carry an RNA-dependent RNA-polymerase (RdRp)
within its capsid.
• Upon entrance into the host cell, the plus-strand RNAs generated by the
RdRp are used as mRNA for protein production.
• When viral genomes are needed the plus-strand RNAs are used as
templates to make minus-strand RNA.
RNA viruses (Class III, IV, V, VI)
• Class VI: +ssRNA, retroviruses (With ds DNA intermediate)
• Despite the fact that the retroviral genome is composed of +ssRNA, it is
not used as mRNA. Instead, the virus uses its reverse transcriptase to
synthesize a piece of ssDNA complementary to the viral genome.
• The reverse transcriptase also possesses ribonuclease activity, which is
used to degrade the RNA strand of the RNA-DNA hybrid.
• The reverse transcriptase is used as a DNA polymerase to make a
complementary copy to the ssDNA, yielding a dsDNA molecule. This
allows the virus to insert its genome, in a dsDNA form, into the host
chromosome, forming a provirus.
• Unlike a prophage, a provirus can remain latent indefinitely or cause the
expression of viral genes, leading to the production of new viruses.
PART 3: Viral genetic Variations
• Viruses grow rapidly.
• A single particle produces a lot of progeny.
• DNA viruses seem to have access of proof reading enzymes, RNA
viruses do not have
Variations (or even appearing a new virus can occur as a result of):
1. Mutation
2. Recombination
1- Mutations
Origin of mutations
1- Spontaneous mutation
• Polymerase errors (Mutations rates are higher in RNA viruses because of
the lack of proof reading enzymes)
• Tautomeric form of bases
2- Physically or Chemically induced
• Types of mutations:
• Point (Silent, missense, nonsense mutation)
• Insertion (Frameshift mutation)
• Deletion
Phenotypic changes seen in virus mutants
• Plagues size, may be larger or smaller than in the wild type virus
• Drug resistance: the possibility of drug resistant mutant arising must
always be considered
• Enzyme-deficient mutant: some viral enzymes are not always essential
and so we can isolate viable enzyme-deficient mutants.
• They may be more virulent as a result of mutations
• Attenuated mutants (cause milder symptoms and may be used to
develop vaccine)
2- Recombination
• Viral recombination occurs when viruses of two different parent strains coinfect
the same host cell and interact during replication to generate virus progeny that
have some genes from both parents.
• Exchange information between two genomes
Thank you