General Virology

Question 1

What is virus?

Answer 1

Viruses are infectious agents of small size (range 20-300 nm) and simple
structure, able of multiplying in animal, plant, fungal and bacterial cells,
exploiting their biosynthetic apparatus

Viruses, outside the cells, are aggregates of biologically inert
macromolecules, whose genetic information is propagated within suitable
cells
They possess no functional organelles and strictly depend on their cellular
host
Viruses are able to alternate two distinct states: intracellular and extracellular

Question 2

________________ is required for virus observation

Answer 2

Electron microscopy

Question 3

Viral morphology

Answer 3

• ovoid or rectangular viruses
• rounded viruses
• filamentous viruses
• bullet viruses, etc.

Question 4

Viral structure:

Answer 4

The complete extracellular viral particle is called a virion
The virion is composed of a nucleic acid (either DNA or RNA)
and a protein coat, the capsid
capsid + viral genome = nucleocapsid
The capsid protects the genome and it is made up of subunits
called capsomeres (composed of protomers/proteic subunits)
Outside the nucleocapsid, in some viruses, there is a lipoprotein
membrane, the envelope, derived from the host cell

Question 4

Bacteriophage structure

Answer 4

Different features:
A) Contractile tail, dsDNA (T2, T4);
B) Long tail not contractile, dsDNA (T1, λ);
C) Short tail not contractile, dsDNA (T3);
D) Without tail, large capsomers, ssDNA (φχ 174);
E) Without tail, small capsomers, ssRNA (MS2);
F) Without head, filamentous, ssDNA (M13)

Question 5

Virion Structure: Naked Capsid
Icosahedral (cubic) symmetry

Answer 5

Icosahedron: 12 vertices. 30 edges, 20 faces

In smaller viruses (i.e., Poliovirus)
protein subunits form trimers
organized into pentamers (or pentons)
Capsid assembly of the icosahedral capsid
of a picornavirus.
Individual proteins associate into subunits,
which associate into protomers,
capsomeres, and an empty procapsid.
Inclusion of the (+) RNA genome triggers its
conversion to the final capsid form

Question 6

Virion Structure: Naked Capsid
Icosahedral (cubic) symmetry

Answer 6

Larger capsid virions are constructed by
inserting structurally distinct capsomeres
between the pentons at the
vertices. These capsomeres have six
nearest neighbors (hexons).
In medium-sized viruses 12 pentamers
are localized at the vertices of the
icosahedron and 20 hexons are localized
on the faces (i.e., Caliciviruses).
Larger viruses have 12 pentons at the
vertices of the icosahedron and a variable
number of hexons on the faces and edges
(60 for Papillomaviruses and
Polyomaviruses, 150 for Herpesviruses,
240 for Adenoviruses)

Adenovirus:
12 pentons with fibers and 240 hexons

Question 7

Virion Structure
Helical symmetry

Answer 7

Helical structures appear as
rods, and are observed
within the envelope
of most negative-strand
RNA viruses

Question 8

The envelope

Answer 8

It is a lipid bilayer containing highly specialized viral proteins (glycoproteins and
matrix proteins)
It is acquired by budding through cellular membranes
Presence of antigens important for the immune response
Glycoproteins functions:
* mediate the interaction of the virus with the target cell (viral attachment
protein, VAP*)
* allow the fusion of the envelope with the cell membrane
Matrix proteins functions:
* connect the viral nucleocapsid with the glycoproteins and provide added
rigidity to the virion
* play a fundamental role in the assembly of virions
* In naked capsid viruses, specific capsid proteins function as VAPs

Question 9

Naked capsid viruses:

Answer 9

1)Component: Protein
2) Properties: resistant to temperature, acid, proteases, detergents, drying
3) Consequences: easily spread, can dry out and retain infectivity, can survive the adverse conditions of the gut, resistant to detergents, antibody might be sufficient for immunoprotection.

Question 10

Enveloped viruses:

Answer 10

1) Components: membrane, lipids, proteins, glycoproteins
2) properties: disrupted by acid, detergents, drying, heat
3) consequences: cannot survive the gastrointestinal tract, spreads in large droplets, secretions, organ transplants, blood transfusions; doesnt need to kill the cell to spread, may need antibody and cell-mediated immune response for protection, elicits hypersensitivity and inflammation to cause immunopathogenesis

Question 11

Viral nucleic acid:

Answer 11

The viral genome is a single nucleic acid (haploid, except Retroviridae) DNA or RNA
(monocatenary or bicatenary; circular or linear; whole or segmented)

Question 12

Double-stranded DNA (dsDNA) viruses:

Answer 12

Linear (Herpesviridae, Adenoviridae, Poxviridae)
Circular (Papillomaviridae, Polyomaviridae)

Question 12

Single-stranded DNA (ssDNA) viruses:

Answer 12

Linear (Parvoviridae)

Question 13

Partially double-stranded DNA

Answer 13

Circular with a break on a filament
(Hepadnaviridae)

Question 14

Single-stranded RNA viruses:

Answer 14

Linear, positive (Coronaviridae, Flaviviridae, Togaviridae, Matonaviridae,
Astroviridae, Caliciviridae, Picornaviridae)
Linear, negative (Paramyxoviridae, Rhabdoviridae, Filoviridae)
Linear, negative or ambisense, segmented (Arenaviridae, Bunyavirales)
Linear, positive, diploid (Retroviridae)
Linear, negative, segmented (Orthomyxoviridae)

Question 14

What are positive and negative RNA viruses?

Answer 14

Positive and negative sense RNA viruses are the two types of ssRNA viruses. Positive sense RNA viruses have a genome containing viral mRNA that can be readily translated into proteins. However, negative sense RNA viruses consist of a genome containing viral RNA that is complementary to the mRNA.

Question 15

Double-stranded RNA viruses:

Answer 15

Linear, segmented (Reoviridae)

Question 16

Viral proteins:

Answer 16

• Structural proteins
• Proteins regulating some functions or components of the host cell (e.g., the
  transcription of cellular DNA) to the advantage of the virus
• Polymerases for nucleic acid replication (DNA or RNA polymerases)
• Enzymes that:
• regulate the interaction with the surface of the host cell (neuraminidase);
• transcribe the viral genome into mRNA (DNA-dependent RNA polymerase);
• add end groups to the viral mRNA (poly (A) polymerase);
• copy the viral RNA to DNA (RNA-dependent DNA polymerase);
• other functional enzymes (protein kinases)

Other chemical constituents….
Lipids are present in the envelope, where a small amount of protein-bound
carbohydrates is also found

Question 17

Classification of viruses
Classification based on structural, physicochemical
and replicative characteristics

Answer 17

Properties of virions
Properties of the genome
Properties of viral proteins
Replicative properties of the genome
Physical properties
Biological properties

Question 18

Properties of virions:

Answer 18

Dimensions
Form
Presence of envelope
Symmetry of the capsid
Structure of the capsomers

Question 19

Properties of the genome:

Answer 19

Type and size of the nucleic acid
Mono / bicatenary
Linear / circular
Positive, negative or ambisense
Number and size of segments
Presence of cap-5’ terminal
Presence of covalently linked 5’ terminal polypeptide
Presence of poly(A)-3’ terminal
Nucleotide sequence

Question 20

Replicative properties of the genome:

Answer 20

Nucleic acid replication strategy
Characteristics of transcription
Translation and post-translation processing features
Site of protein accumulation, assembly and maturation
Cytopathology
Formation of inclusions

Question 20

Properties of viral proteins:

Answer 20

Number of proteins
Protein size
Functional activities of proteins
Amino acid sequence

Question 21

Physical properties:

Answer 21

Stability to pH Thermal stability Stability to cations Stability to solvents Stability to detergents Radiation stability

Question 22

Biological properties:

Answer 22

Serological correlations Host spectrum Pathogenicity Tissue tropism Transmission Relationship with vectors Geographical distribution

Question 22

Enteric viruses:

Answer 22

Viral agents acquired by ingestion that multiply in the intestinal tract: Families Reoviridae, Coronaviridae, Picornaviridae, Adenoviridae, and Caliciviridae

Question 23

Respiratory viruses:

Answer 23

Viral agents acquired by inhalation that multiply in the respiratory tract: Families Orthomyxoviridae, Paramyxoviridae, Coronaviridae, Adenoviridae, and Picornaviridae

Question 24

Neurotropic viruses:

Answer 24

Viral agents acquired through different ways that multiply first at the site of entry and in other organs recognizing their final target in the nervous system: Families Picornaviridae, Rhabdoviridae, Paramyxoviridae, Herpesviridae, Arenaviridae, Polyomaviridae, and Arbovirus

Question 25

Dermotropic viruses:

Answer 25

Viral agents acquired through different ways that multiply first at site of entry and in other organs recognizing the final target in the skin or mucous membranes or that multiply exclusively at the level of the skin/mucous membranes: Families Poxviridae, Paramyxoviridae, Herpesviridae, Picornaviridae, Matonaviridae, and Papillomaviridae

Question 26

Arboviruses:

Answer 26

Viral agents that multiply in bloodsucking arthropods and are transmitted through their sting to a vertebrate host: Families Togaviridae, Flaviviridae, Reoviridae, and Bunyaviridae

Question 27

Oncogenic viruses:

Answer 27

Viral agents that are acquired by different modes of transmission, have a specific tissue tropism and establish persistent infections causing transformation or immortalization of the cells: Families: Herpesviridae, Poxviridae, Adenoviridae, Polyomaviridae, Papillomaviridae, Hepadnaviridae, and Retroviridae

Question 28

Steps in viral replication:

Answer 28

1. Recognition of the target 2. attachment 3. penetration 4. uncoating 5. macromolecular synthesis a) early mRNA and nonstructural protein synthesis: genes for enzymes and nucleic acid-binding proteins b) replication of the genome c) late mRNA and structural protein synthesis d) posttranscriptional modification of protein 6. assembly of virus 7. budding of enveloped viruses 8. release of virus

Question 29

Adsorption or Attachment:

Answer 29

Adsorption involves the attachment of viral surface proteins or glycoproteins to the receptors on the target cell surface This step determines the preferential virus infectivity for certain tissues of the host organism However * some viruses recognize more than one receptor; * different receptors can act in sequence (first contact and subsequent stabilization); * the cell entry of some viruses could be receptor-independent. Some viruses (e.g., HIV) have a double attachment process, involving co-receptors: Phase 1: low binding affinity with a cell receptor which has the purpose of bringing the virus closer to a second cell receptor Phase 2: the second cell receptor promotes the formation of a strong bond and the virus initiates the penetration

Question 30

Virus penetration into the target cell:

Answer 30

While attachment also occurs at 4°C, virus penetration occurs only at 37°C and requires energy The phenomenon is still poorly understood in its molecular details. Different viruses use a preferential entry mechanism Some enveloped viruses enter cells by direct fusion of plasma membrane and envelope Lipids and proteins of the viral envelope are incorporated into the cytoplasmic membrane, allowing the entry of the nucleocapsid into the cytoplasm Fusion glycoproteins are present on the viral envelope

Question 31

Enveloped virus penetration by fusion:

Answer 31

Subsequent steps of adsorption, fusion of the envelope with the plasma membrane of the target cell, and release of the nucleocapsid into the cytoplasm

Question 32

Virus endocytosis by target host cell:

Answer 32

Other enveloped (and naked viruses) are taken in by receptor-mediated endocytosis (viropexis) The viruses (enveloped and not) engaged in receptormediated endocytosis are inserted into clathrin-coated (or caveolin-coated or uncoated) vesicles which, after removal of the coat, fuse with endosomes. Enveloped viruses will fuse their envelope with the membrane of the endosome.

Question 33

In some cases, only the genome penetrates into the target cell: __________________

Answer 33

Pore-mediated penetration of Picornaviridae genome

Question 34

Translocation or direct penetration:

Answer 34

Following a conformational change (invagination) of the cytoplasmic membrane some viruses spontaneously enter the cell, without interacting with cell receptors

Question 35

The nucleic acid of_____________________ enters the cell by direct injection,

Answer 35

bacteriophages

Question 36

Uncoating:

Answer 36

Process that allows the exposure of viral nucleic acid and the subsequent beginning of the synthesis processes; viral and cellular enzymes can participate in this process

Question 37

Macromolecular synthesis Site of viral replication:

Answer 37

Depending on the type of nucleic acid and its characteristics, viruses replicate in different ways and districts (cytoplasm, nucleus) of the host cell Viruses with a DNA genome replicate in the nucleus Exception: poxviruses replicate in the cytoplasm because they have their own DNA-dependent RNA polymerase Viruses with an RNA genome replicate in the cytoplasm Exception: retroviruses and influenza virus replicate in the nucleus

Question 38

Viral gene expression:

Answer 38

Viruses can synthesize a molecule of mRNA for each gene (monocistronic RNA), or mRNA that include the information of multiple genes, which will give rise to polyproteins that will be subsequently cleaved Early translation (nonstructural proteins) proteins translated from mRNAs transcribed from the genome of the infecting virus enzyme for nucleic acid replication regulatory proteins Late translation proteins translated from mRNA transcribed from the newly synthesized viral genome viral structural proteins proteins inhibiting early protein synthesis and replication of viral nucleic acids

Question 39

Replication of the viral genome:

Answer 39

Some DNA viruses use their DNA-dependent DNA polymerase (Adenoviruses, Herpesviruses, Poxviruses), while others use the cellular DNA polymerase (Polyomavirus, Parvovirus, Papillomavirus) All RNA viruses have their own enzymes for their replication (RNA-dependent RNA polymerases, replicases and transcriptases) Negative-strand and double-strand RNA viruses bring the machinery for these processes into the cell together with the genome as part of the nucleocapsid Hepadnaviruses and Retroviruses have a peculiar enzyme for their replication (RNA-dependent DNA polymerase or reverse transcriptase)

Question 40

Replication of Retroviruses:

Answer 40

diploid genome consisting of two identical positive-sense linear ssRNA molecules * Viral reverse transcriptase (dsDNA) and integrase * Cellular DNA-dependent RNA polymerase produces the transcripts (subgenomic and genomic)

Question 41

Replication of Herpes simplex virus:

Answer 41

1) Attachment and Entry: HSV binds and fuses with the host cell membrane. 2) Transport to the Nucleus: The capsid moves to the nucleus, where DNA is released. 3) Gene Expression: IE, E, and L genes are expressed in stages, controlling replication. 4) DNA Replication: Viral DNA is replicated in the nucleus. 5) Assembly and Envelopment: New virions are assembled and acquire their envelope. 6) Release: Virions exit the cell through exocytosis, potentially causing cell death. 7) Latency: HSV establishes latency in neurons and can reactivate

Question 42

Replication of Parvoviruses:

Answer 42

Linear ssDNA * the cells must be actively multiplying and in S phase * cellular DNA polymerase makes the bicatenary genome (replicative intermediate) * Cellular DNA-dependent RNA polymerase II makes the transcription * a viral protein cuts the dsDNA giving rise to two chains of which the original one, devoid of the repeated sequences transferred to the newly formed molecule, is then completed in 3‘; * the two chains are then separated by helicases, leading to the formation of two molecules that begin a new replicative cycle

Question 43

Replication of Hepatitis B virus:

Answer 43

* Genomic DNA (L+S strand) enters the nucleus and is converted to dsDNA; * the filament L serves as a template for transcription by cellular DNA-dependent RNA polymerase II; * two types of mRNA are formed: pregenomic RNA (replicative intermediate) and subgenomic RNA (mRNA for protein synthesis); * encapsidated by core proteins, the pregenomic RNA is retrotranscribed into a singlechain DNA by the viral DNA polymerase and then degraded by it (ribonuclease activity); * the synthesis of the filament S follows

Question 43

Replication of +RNA viruses: Astroviridae, Caliciviridae, Picornaviridae, Coronaviridae, Flaviviridae, Togaviridae

Answer 43

Linear positive ssRNA * Viral RNA acts as mRNA * the viral RNA-dependent RNA polymerase is translated * The polymerase generate a replicative intermediate linear negative ssRNA to generate a new positive-sense genome

Question 44

Virion release by budding (enveloped viruses):

Answer 44

Human-enveloped viruses acquire lipid bilayer membrane by budding from a cellular membrane The exit from the cell occurs through exocytosis (in the case of envelope formation across intracellular membranes) or budding at the level of the cytoplasmic membrane, in some cases also enveloped viruses can be released by cell lysis Acquisition of the lipid bilayer membrane by budding from a cellular membrane. Viral spikes are expressed on the cell surface followed by synthesis of matrix protein that associates near the plasma membrane where viral spikes are present. The matrix protein attracts the assembled nucleocapsid (genome + nucleoprotein) near the plasma membrane expressing viral spikes followed by envelope membrane wrapping and release of the virus particle The initial budding rarely causes cell death but many progeny viruses released result in loss of cell membrane permeability

Question 45

Assembly of naked capsid viruses and nucleocapsids:

Answer 45

Capsids and nucleocapsids selfassemble from preformed capsomeres Icosahedral capsids are preassembled and the genomes are complexed with condensing proteins The process of enclosing the viral genome in a protein capsid is called encapsidation Helical nucleocapsids are assembled by adding protein subunits to the RNA genome to form a helix

Question 46

For _____ viruses (without envelope) the cell membrane lyses and releases the virions

Answer 46

lytic

Question 47

Each infected cell may produce as many as 100,000 particles; however, only ________ of these particles may be infectious. The yield of infectious virus per cell, or burst size, and the time required for a single cycle of virus reproduction are determined by the properties of the virus and the target cell

Answer 47

1% to 10%