9- Taxonomy of Viruses

Question 1

Virus taxonomy; classification

Answer 1

• Viruses are grouped into families (end in “-viridae”). Ex.: Retroviridae
• Viruses are given a genus name (end in “-virus”). Ex.: LenDvirus
• Viruses are given a species name (usually in english). Ex.: Human immunodeficiency virus.

• Classification is based on characteristics:
– Nature of the host (animal, plant, bacteria, etc.). Ex.: bacteriophages infect bacteria.
– Type of disease caused (enteric, leukemia, pneumonia). Ex. Murine leukemia virus
(MLV).
– Life cycle (pathways of nucleic acid replication and transcription).
– Naked or enveloped
– Type of nucleic acids and strandedness (+ strand: same as mRNA)

Question 2

What is the Baltimore classification scheme?

Answer 2

• Classification is based on the type of genome. It is useful because the kind of genome will dictate the replication mechanism.

• RNA genomes:
– Plus configuration: same strand than mRNA (can be translated directly).
– Minus configuration: complementary to mRNA (needs to be transcribed into plus strand before it can
be translated).

Question 3

What is the life cycle of viruses? Adsorption; Penetration’ Uncoating

Answer 3

• Adsorption: attachment of the virus to specific receptors on the surface of the cell.
Plant viruses are usually introduced into the host by insect vectors, or following
mechanical damage.

• Penetration: virus genome enters the cell.
– In enveloped and naked viruses, the complete virion may enter the cell.
– In enveloped viruses, the envelope may be left at the cell surface such that only the
nucleocapsid enters the cell.
– In naked viruses, the nucleocapsid may be left at the surface.

• Uncoating: removal of the envelope and\or the nucleocapsid by host enzymes,
sometimes within lysosomes (in eukaryotes).

Most enveloped viruses of
eukaryotes use endocytosis
(viropexis). Such viruses are
then delivered to lysosomes
which degrade the nucleocapsid and the nucleic
acid is release into the cytoplasm.

Question 4

What is the life cycle of viruses (part 2)? Replication; maturation; release

Answer 4

• Replication of the nucleic acid, transcription and protein synthesis.

• Maturation: assembly of virus
components, nucleic acid,
nucleocapsid and accessory proteins to form new virions. Usually, the assembly is spontaneous (occurs by itself).

• Release : mature virions exit the host cell by means of budding or by causing lysis of the cell. Plant viruses exit and
are transmitted by means of vectors.

Question 5

Virus replication; latent period; elipse; maturation; release (rise period); bursy size

Answer 5

Latent period: eclipse + maturation

• Eclipse: time necessary for the host cells to replicate the viral genome and to synthesize the viral components.

• Maturation: time needed for the different components to be
assembled.

• Release (Rise period):
– Virions are detected outside the cell.
– Lysis: virus-encoded proteins
damage the cytoplasmic membrane.
In bacteria, a virus-encoded protein destroys the peptidoglycan layer.
– Budding (enveloped virus)

• Burst size: number of virions released (varies according to the virus, host cell, etc.).

Bacterial virus: 20-60 min.
Animal virus: 8-40h.

Question 6

What is bacteriophage?

Answer 6

Best-studied bacteriophages infect E. coli (Gram-negative).
• Most phages contain linear dsDNA genomes. Most are naked, but some possess lipid envelopes.
• Viral Life Cycles
– Virulent phages: replication results in host cell lysis (lytic pathway): T4.
– Temperate phages: the genome becomes incorporated into the
bacterial host genome (lysogenic pathway): Lambda.

Question 7

What is T4?

Answer 7

Virulent phages: replication results in host cell lysis (lytic pathway)

Question 8

Bacteriophage T4; adsorption

Answer 8

Adsorption: T4 attaches to the core region of LPS by the tail fibers.
• Following attachment, the tail sheath contracts, forcing the central core through the outer membrane. Tail lysozymes digest the peptidoglycan layer, forming a small pore.
• The phage DNA is then injected into the cytoplasm of the host cell.

Question 9

Explain Bacteriophage Lambda replication (temperate phage); prophage; lysogen

Answer 9

Infection by temperate phages results in a prolonged, latent state of infection (lysogeny). The phage is carried on the
chromosome.

• Prophage: phage genome within the host cell chromosome.
• Lysogen: bacterium that contains a prophage.

• Sometimes, the prophage can exit the chromosome (a process called excision)
and continue along the lytic pathway, resulting in the production of new virus
particles and host cell lysis.

Question 10

Explain Single-stranded DNA phage

Answer 10

Phage ΦX174 is a plus strand DNA phage (same strand as mRNA). The minus strand must be synthetized first to produce a dsDNA genome, the
replicative form.

Question 11

Explain Single-stranded RNA phage

Answer 11

• Phage MS2 is a plus strand RNA phage (same strand as mRNA). For replication, the minus strand must be synthesized first.

• The genome is first used as an mRNA and directs the synthesis of an RNA replicase (RNA-dependent RNA
polymerase, this funcDon is not
performed by the host) and other viral proteins.

• The RNA replicase synthesizes a minus
strand RNA that is used to produce additional mRNA and additional copies of the genome (plus strand) for
the production of new virions.

Question 12

Explain DNA genome; penetration; host transcription/translation apparatus
synthetizes; ssDNA

Answer 12

• Example: Herpesvirus
• Penetration: fusion of the cell cytoplasmic membrane with the virus envelope. Nucleocapsid is transported to the nucleus where viral DNA is uncoated.

• Host transcription/translation apparatus synthetizes:
– Immediate early proteins (transcription factors and,
in some cases, virus-specific RNA polymerase).
– Delayed early proteins (viral-specific DNA polymerase, and other viral proteins necessary for replication.
– Late proteins: nucleocapsid

• Assembly occurs in the nucleus, envelope is
added via a budding process through the inner membrane of the nucleus. The complete virions are then secreted out of the cell by the ER-Golgi pathway.

• ssDNA genome: first converted to a dsDNA
replicative form.

Question 13

Explain RNA genome: 1. plus-strand RNA

Answer 13

• Example: Poliovirus, Hepatitis A virus.
• The genome can be translated directly.
• In Poliovirus, the plus-strand RNA serves as a template for synthesis of a large polyprotein that is cleaved into proteins.

Question 14

What poliomyelitis?

Answer 14

Paralytic polio in 1% of cases.
Skeletal deformities post-paralytic polio.
No cure, but safe and effective vaccine.

Question 15

Explain RNA genome 2. minus-strand RNA

Answer 15

• Example: Measles, Rabies
(Rhabdovirus), Influenza
(Orthomyxovirus).

• The genome cannot be translated directly. The RNA genome (minusstrand)
is first transcribed into a plusstrand RNA by an RNA-dependent RNA polymerase carried inside the virions.

Question 16

What measles?

Answer 16

1963: Nearly all children got measles
before 15 yo. 3-4 million cases/year, 500 death, 48,000 hospitalization, 4000 encephalitis.

Severe complications:
• Pneumonia: 1 in 20
• EncephaliDs (deafness, intellectual
disability): 1 in 1000
• Death: 1-2 in 1000

Long term complication:
• Subacute sclerosing panencephalitis
(SSPE): fatal neurodegenerative
disease, 4-11 in 100,000
Safe and effective vaccine.
hUp://www.cdc.gov/measles/index.html

Question 17

Explain RNA genome 3. dsRNA

Answer 17

• Example: Rotavirus (Reovirus).

• The dsRNA genome can not be translated. First, a plus-strand RNA must be
synthetized by a viral-encoded RNA-dependent RNA polymerase using the minus
strand as the template.

• The plus-strand is then translated into proteins and is used as a template to
synthesize a minus strand to yield dsRNA genomes.

Question 18

Explain RNA genome - retrovirus

Answer 18

• Example: HIV.
• Causing cancer: Rous sarcoma virus.

• The virion carries two identical copies of the
genome (plus-strand ssRNA), reverse transcriptase, integrase and proteases.

• The reverse transcriptase is an RNAdependent DNA polymerase that reverse
transcribes the RNA genome into DNA.

• The DNA genome travels to the nucleus and is integrated into the host DNA.

• LTR: long terminal repeats. Contain promoters for transcription and participate in
the integraDon process.

• Provirus: integrated viral DNA. Contrary to the lambda prophage, the provirus cannot
excise from the host genome.

Question 19

Explain cell fusion?

Answer 19

Enveloped viruses that fuse with the host cell cytoplasmic membrane carries viral
proteins that fuse biological membranes.

• Cell fusion results in hybrid cells that have chromosomal aberraDons, and are
usually short-lived.

Question 20

Explain Oncogenic/tumor-producing viruses

Answer 20

Some viral infection are implicated in the conversion of a normal cell into a tumor
cell, i.e. a cell that has acquired immortality, characterized by uncontrolled replication. This process is
called transformation.

• Both DNA and RNA viruses are known to cause tumors in animals and in humans.
In most cases, other factors are also involved. Viruses are not the only cause of cancer.

Question 21

What are the mechanism for Oncogenic/tumor-producing viruses

Answer 21

Four different mechanisms:

1. Transduction.
2. Insertion of a strong promoter.
3. Inactivation of a tumor suppressor gene
4. Expression of a viral protein that induces transformation (DNA virus)

Question 22

Explain transduction

Answer 22

• RNA virus.
• Example: Rous Sarcoma Virus (avian)

• The virus carries one or many oncogenes (tumor-causing genes), called v-oncogenes
(for virus-encoded oncogene). The voncogene was acquired from the host. This process is called transduction.

• Oncogenes are similar to normal genes found in eukaryotes, known as protooncogenes or c-oncogenes. The protooncogene
is usually involved in the
regulation of the cell cycle or in safety mechanisms that prevent transformation.

• High expression of the oncogene affects the regulation of replicaDon and/or cell death and causes transformaDon.

Question 23

Explain Insertion of a promoter

Answer 23

Retrovirus
• The virus does not encode an oncogene.

• Insertion of a strong promoter of the provirus next to a proto-oncogene (c-onc). The
proto-oncogene is then expressed at high levels and results in misregulartion of the
pathway that prevents transformation. The site of integration of the provirus is very important and transformation will occur only if a proto-oncogene is affected.

Question 24

Explain Inactivation of a tumor suppressor gene

Answer 24

Retrovirus

• The virus does not encode an oncogene.
• Insertion of the provirus in a gene involved in the regulation of proto-oncogene expression. Insertion causes inactivation of the gene and uncontrolled expression of the proto-oncogene, resulting in transformation.

Question 25

Explain Expression of a viral protein

Answer 25

• DNA virus.
• The viral protein does not have a cell counterpart.
• Integration of the viral genome into the host genome may occur (such as in the case of adenovirus, dsDNA) or the viral genome may persist in the cell as an extrachromosomal episome.

• Some DNA viruses that cause tumors do so because they have infected a nonpermissive host, in which they cannot complete their infection cycle. The cell is infected and undergoes uncontrolled replication. Because the virus cannot complete its replication, the cells will never die.
• Example: Human papilloma virus (HPV)
– Gene E6 and E7 induce transformation.