Viruses

Question 1

What are viruses

Answer 1

Biological entities unable to reproduce independently
Carry their nucleic acid within a protein shell
Do not have 16s and 18s rRNAs and so lack ribosomes
Not considered to be true living microbial organisms
Have no ability to make proteins – rely on the hosts translation machinery to make viral proteins that are assembled in the viral progeny
Infectious agents
Host dependent
Vectors for treatment of disease
Driver of evolution
Complex viruses include a core envelope surrounded by additional envelope layers
Virus – genetic element that cannot replicate independently of a living host cell
Virus particle (virion) – extracellular form of a virus, exists outside host and facilitates transmission from one host cell to another, contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material
Viruses display many different shapes and sizes
Most viruses are smaller than prokaryotic cells and range from 0.02 to 0.3 micrometres = 20 to 300 nm

Question 2

Viruses carry their nucleic acid within capsid

Answer 2

Nucleic acid = RNA or DNA, single or double stranded
Capsid – a proteinaceous shell made from structural subunits known as capsomers, some viruses have their capsid surrounded by an envelop made of proteins, lipids and carbohydrates

Question 3

Virion structure

Answer 3

Nucleocapsids are constructed in highly symmetric ways:
Helical symmetry – rod-shaped viruses (e.g tobacco mosaic virus), length of virus determined by length of nucleic acid, width of virus determined by size and packaging of protein subunits
Icosahedral symmetry – spherical viruses (e.g human papillomavirus), most efficient arrangement of subunits in a closed cell, may be combined as head and tail (e.g T4)
Some virions contain enzymes critical to infection:
- Lysozyme – makes hole in cell wall, lyses bacterial cell
- Nucleic acid polymerases
- Neuraminidases – enzymes that cleave glycosidic bonds, allows liberation of viruses from cell

Question 4

Nucleocaspid and envelope

Answer 4

Nucleocapsid – complete complex of nucleic acid and protein packaged in the virion
Enveloped virus – virus that contains lipid bilayer with embedded proteins around the nucleocapsid

Question 5

The viral envelope

Answer 5

Made of proteins, lipids and carbohydrates
Proteins are encoded by the viral genome
Lipids and carbohydrates derive from the host cellular membrane (e.g the nuclear and plasma membrane, endoplasmic reticulum, golgi membrane)
These cellular components (carbohydrates and lipids) are picked up by the virus as it extrudes through the host membrane

Question 6

Viral budding through plasma membrane

Answer 6

1. The host cell membrane before or early in the infection
2. Viral encoded proteins (capsid) associate with the plasma membrane. Viral glycoproteins spikes are incorporated into the membrane
3. Viral nucleic acid and proteins assemble near the membrane, budding begins
4. Budding continues with more viral spikes inserted into the membrane
5. Mature virion (viral particle) is released

Question 7

Viruses classified by

Answer 7

Which nucleic acid they contain
The presence or absence of an envelope
What their host is – bacterial, archaeal, fungal, plant, animal
Their size and shape

Question 8

Bacterial viruses

Answer 8

Bacteriophages are very diverse
Best-studied bacteriophages infect enteric bacteria, e.g E.coli and Salmonella enterica
Most phages contain dsDNA genomes
Most are naked, but some possess lipid envelopes
Structurally complex, containing heads, tails and other components

Question 9

Animal viruses

Answer 9

Entire virion enters the animal cell, unlike in prokaryotes
Eukaryotic nucleus is the site of replication for many animal viruses
Many more kinds of enveloped animal viruses than enveloped bacterial viruses – as animal viruses leave their host cell, they can remove part of the host cells lipid bilayer for their envelope
Viruses may consist of different strains (e.g SEROTYPES)
Vary in virulence and antigen properties
e.g influenza, common cold, polio (RNA) smallpox, hepatitis B, shingles (DNA)

Question 10

Coronaviruses

Answer 10

ssRNA (+sense)
32 kb genome
Largest known RNA virus genome

Question 11

How viruses infect host

Answer 11

Lytic cycle – circular dsDNA is replicated, transcribed and translated into proteins to make the components of the viral progeny. Progeny is released
Lysogenic cycle – circular dsDNA integrates in the chromosome (prophage). The prophage is replicated with the host chromosome and passed to the daughter cells. Environmental stimuli induce phage excision. Lytic cycle begins

Question 12

Lytic cycle

Answer 12

1. Attachment (adsorption) of the virus to a susceptible host cell
2. Entry (penetration) of the virion or its nucleic acid
3. Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
4. Assembly of capsids and packaging of viral genomes into new virions (maturation)
5. Release of mature virions from host cell

Question 13

Lytic cycle step 1 and 2

Answer 13

Attachment of virion to host cell is highly specific
- Requires complementary receptors on the surface of a susceptible host (no infection without receptors or mutated receptors) = host range
- Receptors on host cell carry out normal functions for the cell (e.g uptake proteins, cell-to-cell interaction)
- Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or complexes
Of bacteriophage T4
Bacteriophage T4 – virus of E. coli; one of the most complex penetration mechanisms
- Virions attach to cells via tail fibres that interact with polysaccharides on E. coli tail envelope
- Tail fibres retract, and tail core makes contact with E. coli cell wall
- Lysozyme-like enzyme forms small pore in peptidoglycan
- Tail sheath contracts, and viral DNA passes into cytoplasm
- Capsid is abandoned outside the cell
In human diseases
- Herpesvirus (enveloped) uses proteins in its envelope to bind with the host receptors
- Binding of the host’s receptors triggers fusion of the viral envelope with the hosts cell membrane
- Other viruses directly fuse their envelopes with the cell membrane or enter the cell by endocytosis (e.g influenza virus)
Fusion of the viral envelope with the vesicle membrane, viral DNA/RNA is released from the capsid

Question 14

Lytic cycle step 3

Answer 14

DNA virus – double stranded (dsDNA), single strand DNA (+sense) ((+) ssDNA), single stranded DNA (-sense) ((-) ssDNA)
- dsDNA viruses have their own DNA polymerase encoded in their genome. dsDNA infecting viruses can be transcribed and translated by the host directly
- ssDNA viruses need to acquire the complementary strand to make dsDNA with the host DNA polymerase. dsDNA is then transcribed and translated by the host. Replicated viral DNA is converted back to ssDNA before virion packaging
RNA virus - double stranded (dsRNA), single strand DNA (+sense) ((+) ssRNA), single stranded DNA (-sense) ((-) ssRNA)
- RNA viruses violate the central dogma
- (+) ssRNA viruses can either be translated (acts as mRNA) into proteins directly or can replicate (acts as a genome)
- (+) ssRNA viruses need to be replicated to (-) ssRNA which serves as a template for the new (+) ssRNA genome (progeny)
- (-) ssRNA cannot be translated (act as mRNA) directly into proteins. (-) ssRNA must be converted into (+) ssRNA for both replication and translation
- For replication and translation: (-) ssRNA + RNA replicase = (+) ssRNA (replicating form and mRNA)
- For dispersal: (+) ssRNA + RNA replicase = (-) ssRNA (progeny)
- The plus strands of dsRNA viruses can directly be translated (act as mRNA) into proteins with the help of a viral RNA-dependent RNA polymerase
- For replication and translation: dsRNA + RNA replicase = (+) ssRNA (replicating form and mRNA)
- For dispersal: (+) ssRNA = dsRNA (progeny)

Question 15

Retroviruses

Answer 15

Retrovirus – a virus that uses RNA as its genetic material. When a retrovirus infects a cell, it makes a DNA copy of its genome that is inserted into the DNA of the host cell
(+) ssRNA (infecting virus) = (-) ssDNA = dsDNA = (+) ssRNA (progeny)
Retroviral dsDNA is integrated in the host genome by a viral integrase. Viral mRNAs and proteins are made by the host

Question 16

Lytic cycle step 4 and 5

Answer 16

Nonenveloped viruses:
1. Viral capsomers self-assemble forming the capsid or the head (phages)
2. Viral DNA is packed in the capsid/head
3. In phages, the tail and the tail fibres are assembled
4. Viral proteins degrade the cell membrane and virions are released
In phages:
- Holins make pores in the cell membrane
- Enlysins (with lysozyme activity) degrades the peptifdoglycan layer
- Outer membrane bursts because of the internal osmotic pressure of the cell
- The cell membrane the cell wall are debliterated
In enveloped viruses:
1. Viral capsomers self-assemble, forming the capsid
2. And 3. Viral DNA is packed in the capsid
3. Virions are released by budding

Question 17

Viral modes

Answer 17

Virulent mode – viruses can lyse host cells after infection (lytic cycle)
Temperate mode – viruses replicate their genomes in tandem with host genome and without killing the host (lysogenic cycle)
Temperate viruses – can undergo a stable genetic relationship within the host, but can also kill cells through the lytic cycle
Lysogeny – state where most virus gene are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome

Question 18

Host defence against viruses

Answer 18

Many eukaryotes possess mechanisms to diminish viral infections – e.g immune defence mechanisms, RNA interference
In prokaryotes – CRISPR, restriction enzymes (restriction endonucleases) cleave double-stranded DNA at specific sequences, modification of hosts own DNA at restriction enzyme recognition sites prevents cleavage of own DNA (e.g methylation)

Question 19

Viral counter defence

Answer 19

Viral mechanisms to evade bacterial restriction systems
- Chemical modification of viral DNA (glycosylation or methylation); e.g. T4 DNA contains the modified base
5-hydroxymethylcytosine (DNA is resistant to virtually all known restriction enzymes)
- Production of proteins that inhibit host cell restriction system

Question 20

Antiviral therapies

Answer 20

Acyclovir – most common brand name Zovriax
A synthetic analogue of guanosine
Blocks elongation of viral DNA by the virus-encoded DNA polymerase
Effective against herpesviruses (dsDNA) e.g. cold sores (herpes simplex), chickenpox, shingles (herpes zoster)

Question 21

Mode of action of drugs against HIV/retrovirus

Answer 21

HIV drugs can inhibit multiple viral factors:
- reverse transcriptase inhibitors (RTIs) – stops conversion of viral RNA into DNA
- protease inhibitors - prevent the cleavage of large polypeptides into smaller proteins required for the assembly of virions.
- Integrase inhibitors – stops the insertion of viral genomic DNA into the host chromosome
- Entry inhibitors – bind to cell membrane receptors stopping the HIV virus attaching

Question 22

Viral adaptation by mutation

Answer 22

• Virus do not always replicate precisely so mutations arise with high frequency
• Mutations can be small or major
• Cumulative small mutations or one major can give rise to a different serotype/strain
• Mutations can make virus resistant to drugs
  RNA virus mutates faster than DNA virus
  1. there are no RNA repair mechanisms
  2. RNA replicase (an RNA-dependent RNA polymerase) does not have proof-reading activity (like most of the DNA polymerases).

Question 23

Why viruses matter

Answer 23

• Viruses are the most abundant biological entities in the oceans.
• There are 10 times more viruses than cells in seawater.
• In soil and marine sediments, viruses are more abundant than in seawater. E.g., 1 g of sea sediment contains 1010 viral particles.

Question 24

Viruses play important ecological roles

Answer 24

I. Virus predation keeps the population of microbes at bay, preventing blooms that would disrupt the balance of the ecosystem.
E.g., Like protists, viruses are important bacterial and phytoplankton predators in the ocean (help end cyanobacterial and algal bloom).
II. Prophages (prophage is a bacteriophage genome inserted and integrated into the circular bacterial DNA) alter the host metabolism.
Phage influences on bacterial behaviors including motility, biofilm formation, defense, toxicity, replication, metabolism, sporulation, stress response, and quorum (number) sensing.
ROS = reactive oxygen species, abs = antibiotics, QS = quorum sensing (Hargreaves et al, 2014. Bacteriophage 4 (3): e29866)
III. Phages are major vehicles for horizontal gene transfer between prokaryotes.
Horizontal gene transfer (HGT) is the movement of genetic material between organisms
The process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or phage) is transduction
During synthesis of new phages the phage incorporates some host DNA
Infecting a new host incorporates the phage and the previous host DNA into the new host

Question 25

Virus predation as cure

Answer 25

• Phage therapy or biocontrol
• Higher specificity than an antibiotic
• Typically harmless to human/animal and beneficial microbiota
• Currently not authorized for use in humans