Les virus

Question 1

When and how were viruses initially discovered?

Answer 1

Initially described as “des agents filtrables” by Ivanovsky in 1892

Question 2

What are viruses?

Answer 2

An agent that can be filtered

An obligatory intracellular parasite —> dependant on the machinery of the host for replication

Cannot produce energy or proteins with a host cell

Viral genome made of DNA or RNA

Infectious agent —> composantes individuelles sont assemblées, donc qui ne se reproduit pas par division cellulaire

Question 3

Fun facts about viruses: (6+3)

Answer 3

1. Viruses are not living
2. Viruses must infect other cells to stay alive
3. Viruses must be able to use cellular machinery to produce its own components
4. Viruses must encode for all necessary processes that are not “provided” by the host cell
5. Viral components must be self-assembling
6. Not all viruses can infect all cells or hosts
   
   1. They must be able to enter
   2. Once entered, the cell must have the machinery the virus needs to replicate
   3. Once replicated, the virus must be liberated from the cell to transmit the infection

Question 4

Structure et composition de la particule virale (viron)

Answer 4

Measured in nanometers (nm)

Smallest (18nm —> parvovirus)

Biggest (300nm —> poxvirus)

Rule of thumb: bigger viron = larger genome —> can encode for more proteins

Question 5

How is genetic information contained in a viron?

Answer 5

Genome (nucleic acid) covered by a protective layer of protein (capside)

Genome + capside = nucleocapside

(Icosahédrique, Hélicoïdale, Complexe)

All virons have a nucleocapside with or without an envelope

Question 6

DNA vs RNA in virus:

Answer 6

DNA: single or double strand, linear or circular

RNA: single strand (positive polarity or negative),

• double stranded (reovirus) —> polarité+/–ou double sens
• Segmented or not

Question 7

What are the capsid and enveloppe?

Answer 7

The outermost layer of a virus (either one or the other)

• Constitutes the structure, protection and transmission mechanism of the virus.
• The structures present on the surface of the capsid or envelope allow interaction between the virus and the host cell via a viral attachment protein (VAP) or other structure

If the outermost layer is destroyed —> the virus is inactivated

Question 8

What is the capsid?

Answer 8

Made of proteins

Rigid structure capable of resisting unfavourable environmental conditions

Naked (non-enveloped) viruses are generally resistant to dryness, acidity, detergents, etc (including bile and acid in GI tract)

Symmetric (icosaédrique ou hélicoïdale) or asymétrique (complexe)

Question 9

What is the capside isosahédrique?

Answer 9

Les sous sous-unités protéiques virales s’unissent en protomères. Cinq protomères s’unissent pour former des capsomères (pentamères) qui s’assemblent en capside

Made of 12 capsomeres called pentamères/pentons

Information:

• The Icosahedral capsid resembles a sphere and is made up of an assembly of protein subunits.
• All the faces of the simple icosahedron are identical.
• The nucleic acid is contained in the centre of the capsid which protects it from the environment.
• Larger capsid virions are made by inserting capsomers (hexons) between the pentons.
  
  • Ex: Herpes (12 pentons, 150 hexons), Adenovirus (12 pentons, 240 hexons)

Question 10

What is the capside hélidoïdale?

Answer 10

The protein subunits interact with each other and with the nucleic acid to form a structure that resembles a hollow, rigid or flexible protein rod or cylinder

Question 11

What is the enveloppe?

Answer 11

The envelope is a membrane composed of lipids, proteins and glycoproteins.

• Structure similar to cellular membranes.
• Viral glycoproteins are anchored to the envelope and project out of the surface of the virion, like spikes.
• Some act as viral attachment proteins (VAPs), capable of binding to target cells.
  
  • Are major antigens that can elicit protective immunity
• Easily deactivated by environmental factors (dryness, acidity, detergents, solvents) —> survive in GI tract
• The structure of the envelope can only be maintained in an aqueous solution (must remain wet).
  
  • These viruses are usually transmitted by fluids such as blood, respiratory droplets and tissue.

Question 12

What are the two ways in which viruses can be classified?

Answer 12

1. Nature of their genome:
   
   • DNA or RNA
   • Single or double stranded
   • Segmented or not segmented
   • Linear or circular
2. Structure (morphology):
   
   • Symmetry of the nucleocapsid (icosahédrique, hélicoïdale, complexe)
   • Envelopped or not envelopped
   • Number of capsomers

Question 13

What is the international classification of DNA viruses?

Answer 13

Question 14

What is the international classification of RNA viruses?

Answer 14

Question 15

What is the convention for naming viruses?

Answer 15

Question 16

What are some important members of the DNA virus family?

Answer 16

Question 17

What are some important members of the RNA virus family?

Answer 17

Question 18

Generalities about viral replication:

Answer 18

• The main stages of viral replication are the same from one virus to another
• The host cell acts as a factory, providing the substrates, energy and machinery necessary for viral protein synthesis and genome replication.
• What is not provided by the host cell must be encoded in the virus genome

Question 19

What are the steps of viral replication? (8)

Answer 19

1. Recognition of the target cell
2. Attachment
3. Entry into the cell through the plasma membrane
4. Decapsidation
5. Synthesis of viral constituents (viral multiplication)
   
   1. Synthesis of early mRNA and non-structural proteins
   2. Genome replication
   3. Synthesis of late mRNA and structural proteins
   4. Post-translation modification of the protein
6. Virus assembly
7. Budding of enveloped viruses
8. Release of the virus from the host cell

Question 20

Steps 1 and 2:

Answer 20

1) Reconnaissance et 2) attachement à la cellule cible

Examples of PAVs —> gp120 of HIV, HAgp of the virus

Examples of receptors —> CD4 and chemokine co-receptor on the “helper T-cell” T-lymphocytes for HIV and Sialic acid from epithelial cells for Influenza A

Question 21

Step 3:

Answer 21

No envelope: endocytosis mediated by receptor

Enveloped: fusion of the membranes of the virus and the target cell (whether or not preceded by endocytosis), the nucleocapsid or viral genome is then released into the cytoplasm

Question 22

Step 4:

Answer 22

Decapsidation

After internalization, the nucleocapsid arrives at the site of replication and breaks off.

• The DNA genome is usually transported to the nucleus (exception: poxvirus).
• The RNA genome usually remains in the cytoplasm (exceptions: orthomyxovirus and retrovirus).

Question 23

Step 5:

Answer 23

La synthèse des constituants viraux (multiplication virale)

• Most DNA viruses use polymerases from the host cell to synthesize mRNA in the nucleus (exception: poxviruses).
• RNA viruses replicate in the cytoplasm (except for orthomyxoviruses and retroviruses) and must themselves encode the enzymes necessary for transcription and replication (the host cell does not have what it takes to replicate RNA)
• The cellular machinery necessary for mRNA transcription is located in the cell nucleus

Question 24

Steps 6 and 7:

Answer 24

The site and mechanism of virus assembly depend on where replication has taken place and whether the final structure is that of a naked or enveloped virus.

• DNA viruses are assembled in the nucleus (except poxviruses).
• RNA viruses and poxviruses are assembled in the cytoplasm.
• Viral capsids can be assembled and then filled from the genome or can be assembled around the genome.
• The envelope is acquired during the budding of the virus.
• The ppt of RNA viruses budding from the plasma membrane without killing the cell
• Other viruses acquire their envelope from the endoplasmic reticulum and the Golgi apparatus.
• Errors are made during assembly and result in the formation of virions that are empty or contain a defective genome.

Question 25

Step 8:

Answer 25

**Relâchement hors de la cellule hôte** **Viruses are released from the cell** * By cell lysis * By exocytosis * By budding through the plasma membrane Naked viruses are often released after cell lysis and enveloped viruses are often released by plasma membrane budding without killing the cell. Viruses budding in the cytoplasm are released by exocytosis or cell lysis.

Question 26

What are the main modes of transmission of viruses? (7)

Answer 26

1. Ingestion of contaminated food and water - faecal-oral 2. Fomites 3. Aerosols 4. Direct contact with secretions (saliva, wound) 5. Droplets - Sexual contact 6. Contaminated blood or organ transplantation - Zoonoses (animals, insects) 7. From mother to child: vertical transmission

Question 27

Ecology and transmission of viruses: (3 things)

Answer 27

**The mode of transmission depends on the source of the virus and the ability of the virus to endure the conditions of the environment and the body to its target cell.** * The presence or absence of an envelope is the main structural determinant of the mode of viral transmission. * Unwrapped viruses are resistant to drought, detergents, temperature and pH extremes unlike wrapped viruses **Unenveloped viruses can therefore survive the acidity of the stomach and the detergent effect of the bile acids in the intestine.** * Often transmitted by the fecal-oral route * Frequent source: contaminated objects (fomites) **Enveloped viruses are more fragile: they need an intact envelope to remain infectious and must remain wet.** * Often transmitted by respiratory droplets, mucus, saliva and semen, blood, transplanted organs.

Question 28

What are zoonoses and arboviruses?

Answer 28

**Animals can be vectors:** They can also act as a **reservoir**: they maintain and amplify the virus in the environment. Viral diseases that can affect animals (or insects) and humans are called zoonoses. When **arthropods** (mosquitoes, ticks, flies, etc.) are the **vector** of a viral infection, the infection is an **arbovirosis**.

Question 29

What are some other transmission sources?

Answer 29

**Beware of asymptomatic infections that may contribute to transmission (STBBI)** * Living conditions: overcrowding * Work/leisure * Lifestyles (especially when travelling) * Daycare attendance * Travel

Question 30

How are viruses detected and dx? (4)

Answer 30

**Viral culture** on cells derived from human tissue in a single-cell layer * Characteristic cytopathic effects can be observed - Still used for some specimens * Detection of specific antibodies in the infected host **Serology** [early serum, late serum (acute or latent phase)]. * Very often used **Detection of viral genetic material (PCR)** * _Most used_ Observation in **electron microscopy** - In the research laboratory

Question 31

How are infections controlled? (3 main ways)

Answer 31

Hygiene Vaccination (prevention) * Inactivated, live attenuated, other Antiviral treatment * For certain viral infections only

Question 32

What forms of antiviral treatments are available? (5 kinds)

Answer 32

1. Inhibition of virus attachment to the cell 2. Inhibition of the entry into the cell and 3) of the decapsidation 3. Inhibition of mRNA synthesis 4. Inhibitors of genome replication 5. Assembling the virus and 6) releasing it out of the cell

Question 33

Inhibition of virus attachment to the cell (tx)

Answer 33

**Neutralizing antibodies** * ex: passive immunization against hepatitis B (immunoglobulins) - Specific receptor antagonists **Analogs of cell receptors or VAP that block the interaction between the virus and the cell** * ex: inhibitors of the CCR5 cell receptor that prevent HIV from binding to macrophages and certain CD4 cells.

Question 34

2) Inhibition of the entry into the cell and 3) of the decapsidation (tx)

Answer 34

**If this process is blocked, the virus genome cannot be released into the cell to replicate.** For viruses that do not enter from endocytic vesicles, some antivirals will neutralise the pH of these compartments to prevent fusion or breakage of the membrane preventing decapsidation. * Amantadine and rimantadine (More specific action against Influenza A) * Enfuvirtide that blocks the entry and decapsidation of HIV by inhibiting the fusion protein gp41

Question 35

\*\*\*Inhibition of mRNA synthesis\*\*\* (tx)

Answer 35

**not a good target in general** * mRNA is not a good target since it is difficult to inhibit the mRNA of the virus without inhibiting the mRNA of the host cell

Question 36

4) Inhibitors of genome replication (tx)

Answer 36

**Most antivirals are nucleoside analogues (modified nucleosides)** * **HSV viral DNA polymerase and HIV reverse transcriptase are good examples.** * Ideal therapeutic targets since they are essential for viral replication and are different from host enzymes. * **Nucleoside analogues bind easily to viral polymerase (which is less precise than host enzymes) and inhibit viral replication, usually by stopping the elongation of the DNA or RNA chain** * ex: acyclovir and valacyclovir against HSV, ganciclovir against CMV, lamivudine and zidovudine against HIV.

Question 37

5) Assembling the virus and 6) releasing it out of the cell (tx)

Answer 37

**We want to inhibit the enzymes responsible for these steps** * **Inhibitors of HIV protease**, an enzyme essential to the assembly of the virus and the production of infectious virions. * ex: darunavir and ritonavir * **Influenza A and B neuraminidase inhibitors** (neuraminidase allows the virus to be released outside the cell) * ex: oseltamivir and zanamivir