Lecture 1+2 Introduction to Virology

Question 1

AIDS (Acquired Immunodeficiency Syndrome)

Answer 1

Virus targets the immune system

Question 2

Which viruses are transmitted through air?

Answer 2

Influenza, SARS

Question 3

Which viruses are transmitted through water?

Answer 3

Polio, diarrhea

Question 4

Which viruses are transmitted through contact?

Answer 4

HIV, Ebola, herpes

Question 5

Which viruses are transmitted through food?

Answer 5

Norovirus

Question 6

Which viruses are transmitted through vertical (offspring), germ line?

Answer 6

Plant virus

Question 7

Which viruses are transmitted through mosquito vectors?

Answer 7

Zika, malaria

Question 8

What is a virus?

Answer 8

Smallest genetic entities and their presence often causes infectious disease

• Only visible with electron microscope
• The disease symptoms are needed for the virus to transmit

Question 9

What is the general building plan of a virus?

Answer 9

A piece of genetic information (RNA/DNA) with a protein coat (and sometimes a lipid membrane/envelope) that hijacks the host cell and replicates itself.

The cell will burst open and up to a million replications come free.

Question 10

What are the characteristics of a virus?

Answer 10

• Infectivity: property to penetrate a host cell, to multiply within this cell and to leave the cell and spread to other cells.
• Obligate, intracellular parasite: they cannot replicate by their self. They need a living host cell to replicate –>
  a. No protein synthesizing machinery, they require the cell to produce proteins
  b. No energy producing machinery, no mitochondrion, so requires the cell for this.
• Property to survive outside a living cell in an extracellular state
  a. In an inert state or via carrier
  b. Depends on the environment

Question 11

What is a virus composed of?

Answer 11

Nucleic acid

• RNA (=linear) or DNA
• SS or DS
  Viral genome forms either a single or double-stranded helix
  Double helix: both strands base pair to each other due to complementarity of the nucleotide sequence, similar to the dsDNA genomes of cellular organism
• Segmented or non-segmented

Protein shell: assembled from smaller subunits: the coat proteins

Lipid membrane/viral envelope: Some viruses (HIV), made from the host cell

Question 12

Viral DNA genomes

Answer 12

May be linear or circular.

All viral RNA genomes are linear, except the genomes of viroids. The exact properties of the viral genetic material depend on the family to which the virus belongs.

Question 13

The minimal virus

Answer 13

Need at least 2 genes: DNA- or RNA-polymerase (multiplication of RNA or DNA genome) and a coat protein (protection and host interactions)

Question 14

Some insect viruses

Answer 14

2 genes on 2500 bases-long RNA +ve strand RNA genome (black Beetle Virus)

Question 15

Most complex viruses

Answer 15

100-500 genes of 10^6 bp DNA genome (Herpes-, Pox- and Mimiviruses)

Question 16

Genomes of viroids

Answer 16

Viroids occur in plants and their genomes are even smaller than viral genomes.
Consist of circular, single-stranded RNA with no coding capacity (i.e. viroid genomes do not encode proteins, so need e.g. polymerase).
Viroids are the ultimate “selfish genes”.

Question 17

Viral genome sizes

Answer 17

Varies between 2,000 and 1,000,000 nucleotides

Question 18

Mutation rate

Answer 18

Viruses and viroids have a higher mutation rate than cellular organisms (prokaryotes and eukaryotes).

Mutation rate: number of nucleotide positions per 1000 nt of genome length that mutate per year.

The nature of the genetic material and the number of generations per year affects the mutation rate.

RNA viruses mutate quicker than viruses with a DNA genome

• DNA polymerases (the enzymes that make a complimentary copy from a template DNA), have proofreading ability, which means that they check their work by comparing it to the template.
• RNA polymerases (the enzymes that synthesize RNA) do not have proofreading ability and consequently make more mistakes.

–> This explains why most emerging viruses that threaten human health are RNA viruses

Question 19

Virus classification

Answer 19

Classification according to the genome type (nucleic acid, replication strategy):

• ssRNA, dsRNA, ssDNA, dsDNA
  Families, genera, species
• About 5000 species recognized

Question 20

Single/ double-stranded

Answer 20

As viruses can have ss or ds genomes, the viral genome forms either a single or a double-stranded helix.

In case of a double-stranded helix, both strands base pair to each other due to the complementarity of the nucleotide sequence, similar to the dsDNA genomes of cellular organisms.

Question 21

Virus taxonomy

Answer 21

The official names of virus families end on “viridae”. Names of the genera end on “virus”.

Taxonomy is a theoretical concept that helps to understand evolutionary relationships in biology

Trivial names or when describing the infection process of a virus, italics is not used

Question 22

Segmented/ non-segmented

Answer 22

Segmented: genome divided over several molecules of RNA/DNA

Non-segmented: carry all genetic information on a single RNA/DNA molecule

Question 23

The Viral Coat

Answer 23

Main coat proteins: VP1, VP2, VP3

Nearly all negative-stranded RNA viruses lack a clear protein coat, although a nucleoprotein (N) protects the RNA. These viruses also have a viral envelope that surrounds and protects the genome.

Question 24

The Viral Coat: structural proteins

Answer 24

The viral-encoded proteins that are present in the virus particle (virion) (e.g. coat proteins, nucleoprotein, glycoproteins).

Question 25

The Viral Coat: non-structural proteins

Answer 25

Are not present in the virus particle but are produced after the virus has entered a host cell.

Non-structural (Ns) proteins have crucial roles in the virus replication cycle. These may have essential enzymatic activities (e.g. viral polymerase, protease, helicase, etc.) or affect the host’s immune response, such as interferon antagonists or anti-apoptotic proteins.

The NS proteins are also encoded by the viral genome but are not integrated in the virions.

The RdRP is normally seen as a non-structural protein, but this is not entirely correct for negative-stranded RNA viruses, since a small amount is needed in the virion to initiate the viral replication.

Question 26

The Viral Coat: viral envelope (lipid membrane)

Answer 26

Contains glycoproteins: proteins with complex sugar groups (glycans) attached

• Haemagglutinin (HA)
• Neuraminidase (NA)

Question 27

The Viral Coat: interface

Answer 27

The outer layer of a virus (either the protein coat or the viral envelope containing the glycoproteins) between the virus particle and the host cell surface.

This outer layer executes specific functions in terms of recognizing and binding to suitable host cells and assisting the viral genome to enter these cells.

Question 28

What are the functions of the protein coat?

Answer 28

Protection of the genetic material from decay during the extracellular state of the virus

Recognition and penetration of the host cell

• ‘host range’
• ‘tissue tropism’

Escape from the immune/defence system; avoiding recognition and inactivation

• = minimizing anti-genetic determinants/ variation at surface
  –> The more anti-genetic determinants, the higher the risk of recognition by B-cell receptors and antibodies
• Therefore: pursuing maximal symmetry of protein coat/ lipid envelope
  –> = minimal energy

Question 29

Architecture of viral coats

Answer 29

All virions have a nucleic acid genome covered by a protective layer of proteins, called a capsid. The capsid is made up of protein subunits called capsomeres.

Some viral capsids are simple polyhedral “spheres,” whereas others are quite complex in structure.

Question 30

The viral coat is built up from individual protein subunit

Answer 30

Coat proteins.

• Proteins may have regular structure, but their tertiary structure is never symmetrical
• The required symmetry is realized by regular arrangement of smaller, non-symmetric components.
• Viral coat proteins are encoded by relatively small open reading frames to achieve this. These small units serve as perfect building blocks.

Question 31

The viral coat is built up by smaller subunits

Answer 31

Spherical

• Saving space on the genome
  –> Genetic space reduction
• Increase genetic stability
  –> Small open reading frame; less risk of mutations
  Possibly to self-assembly
  –> Puts itself together
• Structural requirement: assembly symmetric particle from asymmetric proteins

Question 32

Viruses with a protein coat have a … form

Answer 32

Rod-shaped, spherical, or “ complex “ form with a very low degree of morphological variation at the surface. So they comply to the rules of achieving maximal symmetry and minimal surface variation.

Question 33

Structure of a Rod-shaped virus

Answer 33

Asymmetrical, but identical, coat proteins in a circle (disc) → Growing spiral (helical symmetry) in which all subunits are placed in equivalent position relative to each other

Viral genome encapsulated as a spiral or helix

• Size can vary with size of genome to be encapsulated

Question 34

Structure of a spherical virion

Answer 34

Are more symmetrical than rod-shaped viruses

• Icosahedral symmetry
• An icosahedron has 2-, 3- and 5-fold symmetry-axes
  –> Without 5-fold symmetry-axis no perfect globe
  –> Composed of 20 equilateral triangles
• Minimal energy
  –> Maximal symmetry
  –> Protects the nucleic acid

Question 35

Surface of an icosahedron

Answer 35

60 coat protein molecules can be arranged in fully equivalent positions (3 per triangle*20).

In this way, the basic virion is formed, which can also be regarded as being composed of 12 pentamers of coat proteins (arranged around the 5-fold symmetry axes that spreads from the pentagons).

Every icosahedrical capsid is composed of 12 pentameric capsomeres.

Question 36

Triangulation op spherical viruses

Answer 36

All spherical viruses have an icosahedrical building plan, but some viruses are bigger than others → further triangulation in order to create larger spheres to package more DNA or RNA

Larger viruses have a higher triangulation number
–> The triangulation number (T) is a fixed character for a given virus species.

Question 37

Triangulation

Answer 37

20 original equilateral triangles of the icosahedron are subdivided into smaller triangles, allowing many more symmetrical positions for coat proteins.

As a result, there is a slight deviation of the original perfect symmetry. Even if all proteins are chemically identical, some will be in an environment of 5 neighbours as in the basic building plan (pentamers or pentameric capsomers) and others will be in a 6 neighbours environment (hexamers). As the position between subunits is different for pentameric and hexameric arrangements, the term quasi-equivalency has been introduced for triangulated virus particles.

Question 38

T = 3 particles and pseudo T=3 particles

Answer 38

For T=3 particles, the original triangles are divided in 3 smaller triangles. This is the building plan of many small, positive stranded RNA viruses. Here, there are 12 pentameric and 20 hexameric capsomers, made from a total of 180 coat protein molecules.

Poliovirus particles also have such a building plan, but for poliovirus and other picornaviruses, the subunits that build the small triangles are not identical.

Three different proteins, named VP1, VP2 and VP3, are found per triangle and that is why for picornaviruses the term pseudo T=3 is used.

Question 39

Calculating triangulation numbers

Answer 39

Triangulation enables enlargement of the isometric particle. At the same time, it leads to a more perfect and smooth globe.

Some rules for icosahedral viruses:

• The number of pentamers is always 12.
• The number of coat protein molecules divided by 60 gives the triangulation number (T).
• The number of hexamers increases when T increases and can be calculated as 10x (T-1).

Question 40

Coat proteins of icosahedral viruses

Answer 40

Have a similar tertiary structure

In all cases the coat protein contains a large hydrophobic core, rich in ß-sheets, the so-called “eight-stranded anti-parallel ß-barrel”.

The primary structure of the coat protein (amino acid sequence) greatly varies between virus families

Question 41

Atomic structures of viruses

Answer 41

• Helps to understand which parts of the coat proteins are in a position to interact with receptors on the host cell surface.
• Such domains may represent epitopes to which neutralizing antibodies can bind.
  –> Such information is very useful to develop antibody-based antiviral therapies or safe but efficacious vaccines.

Viruses can be purified in certain quantities and it is possible to obtain crystals of pure virus.