Introduction to Viruses

Question 1

Describe the basic features of Viruses

Answer 1

Small infectious agent that replicates by infecting the cells of a host organism

Obligate intracellular pathogens

Size: Ranges 20 - 300 nm

Composed of nucleic acid surrounded by a protein coat

Most viruses can only infeft specific cell types
E.g Skin cells, respiritory cells
This is the virus tropism (nature in which they target)

They have various shapes: icosahedral, helical & complex

Question 2

What are the key components in a mature virus?

Answer 2

Nucleic acid (genome)

Surrounded by a protein coat (capsid)

Some have Virulence factor (embedded proteins)
Help virus enter a cell

Some have lipid envelopes
These can fuse with the lipid envelope on other cells

Question 3

What is the virus genome?

Answer 3

Circular or linear

Can be any of the following:
SS RNA

				DS RNA
				
				SS DNA
				
                                    SD DNA

If it is single stranded it can be either positive or negative sense
-Positive sense
Sequence can code directly for virus protein

-Negative sense
Reverse complement to positive sense doesn’t typically code for protein

*genome type influences how viruses make mRNA

Question 4

What are the functions of the viral proteins?

Answer 4

-Structural proteins encode:
Capsid
outer coat of the virus protects the nucleic acid - may also serve to allow the virus to
bind to target cells **

Nucleocapsid
simpler structure – proteins closely associate with virus genome

Envelope glycoproteins
embedded in lipid membrane of enveloped viruses mediate recognition of host
cells and entry **
** NB Major recognition sites of antibodies
-Non-structural (NS) proteins
Mediate replication of genome
i.e. polymerases

May have role in suppressing the immune system (e.g. NS1 in influenza) or changing 
    the cellular environment

-Accessory Proteins
Special functions, usually in restricted cell types
e.g. orfA in feline immunodeficiency virus promotes replication in lymphocytes

Question 5

What is the lipid envelope?

Answer 5

Derive envelopes from cell membranes by budding

Plasma membrane
	E.g. Influenza, retroviruses
	
Nuclear membrane
	E.g. Herpesviruses

Internal organelles
            E.g. coronavirus

Question 6

What is the clinical relevance of the lipid envelope?

Answer 6

Enveloped viruses tend to be more unstable to heat, pH extremes, detergent

Question 7

Describe the basic features of Prions (TSE)

Answer 7

Prion disease:

Proteinaceous infectious particle (Prion protein: PrP)

Unusual (contentious!) disease 

PrPc is a cellular protein ~250 amino acids.

Expressed mostly in the CNS

Normally exists in one shape (pN) – but can “misfold” (pD) leading to the formation of large protein aggregates. pD seems to propagate more misfolded protein which leads to brain dysfunction and fatal disease

Question 8

How are TSE’s spread?

Answer 8

TSEs are spread by puncture contact, or ingestion.

They can spread by infecting nerve cell ends and lymph cells.

Spleen seems to be a major site of infection prior to CNS

They can also be spread by invasive techniques such as surgery

Question 9

Describe how viruses are classified

Answer 9

Classified based on Genome
Baltimore Classification Scheme

DNA or RNA

Single Stranded or Double Stranded

Negative or Postive sense

Question 10

What does phylogenetics mean in relation to viruses?

Answer 10

Determine how related viruses are to one another

‘study of evolutionary relationships between biological entities’

Uses genetic comparisons between related viruses

Question 11

Outline how Feline Calicivirus is grouped based on its genome sequence?

Answer 11

Determined by:
International committee on taxonomy of viruses (ICTV)

(Order):
Not assigned
Family:
Caliciviridae
(sub family):

Genus:
Vesivirus
Species:
Feline calicivirus

Question 12

How do viruses infect the host?

Answer 12

• Must infect cells which support viral replication
• Require appropriate receptors for cell entry
  Sialic acids for influenza
  Transferrin for feline parvovirus
• Must ensure cell physiology is appropriate
  Supplies replicative enzymes, ATP, nucleotides, other proteins

Question 13

What are the replication strategies of viral replication?

Answer 13

Virus needs to exploit normal cell processes

Either infect specific cells/cell compartments which provide “what they need”

Or encode proteins that they require or which alter the cell metabolism

Question 14

Why do some viruses use polymerase enzymes provided by the host?

Answer 14

Replicate viral genetic material to produce mRNA (protein) and genomic nucleic acid

-provided by cells
	Or
-provided by virus

If suitable polymerase is not provided by cell or not found within the compartment which the virus replicates then the virus must supply polymerase. This is the case with many RNA viruses

Question 15

How does viral ssDNA replicate?

Answer 15

Parvoviruses, circoviruses

Require active host DNA polymerase to replicate genome
i.e. Produce dsDNA
These viruses can only infect dividing cells where DNA polymerase is active

Use host RNA polymerase to produce mRNA

Parvovirus: infect intestinal cells, bone marrow cells, cardiac & neural cells

Question 16

How does viral positive sense ssRNA replicate?

Answer 16

Picornavirus e.g foot & mouth disease

Virus RNA can act directly as mRNA
Genome is directly infectious

RNA translated to produce single polyprotein

This protein is then cleaved by viral proteases

Genome replicated by viral polymerase (through negative sense strand template

Question 17

How does viral negative sense ssRNA replicate?

Answer 17

Virus RNA cannot act directly as mRNA

Virions contain (and genome encodes for)
RNA dependent RNA polymerase

Generates +ve sense mRNA

Genome also replicated by viral RNA polymerase, via +ve sense intermediate

Typically replicate in cytoplasm e.g paramyxoviruses

EXCEPT bunyaviridae and orthomyxoviridae

Question 18

How is retrovirus transcribed?

Answer 18

The viral RNA is reverse transcribed:
viral reverse transcriptase [RNA-dependent DNA-polymerase] converts genome to complimentary DNA (cDNA)

This cDNA integrates into the chromosome of the host cell by viral integrase enzyme:
This integrated DNA is termed proviral DNA

The integrated DNA then produces RNA and protein using normal cell machinery

Integration into host genome is permanent (for life of cell)
Can disrupt normal genome activity and lead to tumour formation

Question 19

Describe how viruses can cause disease

Answer 19

Transformation of normal cells to tumour cells
e.g. feline leukaemia virus & Bovine papilloma virus

Lytic Infection (death of cell & release of infection)
e.g. foot and mouth disease

Persistent infection (slow release of virus without death)
e.g. retroviruses

Latent Infection (virus present but not causing harm to the cell; later emerges into lytic infection
e.g. Herpes virus

Question 20

What are the implications on the animal during a viral infection?

Answer 20

Clinical
Cell death & tissue damage
Host response to infection
Cancer

Sub Clinical
Can cause problems when controlling disease in a population

 Transmission to susceptible animals

 Undetected effects (fertility problems, poor 'form')

 Latent viruses – “hide away” with potential for later disease

Question 21

What are the factors which affect the clinical outcome (virus, host & environment)

Answer 21

Virus:
Virus strain (pathogenicity)
Virus load

Host:
Genetic – immune system genes (e.g. MHC)
Receptors
Age (immune system, receptor expression, dividing tissues, passive immunity)
Pre-existing immunity
Physiological status
Concurrent infection

Environment:
Overcrowding, Ventilation

Question 22

Outline the ways viruses create genetic variation?

Answer 22

Spontaneous mutation
Gene transfer between viruses
Recombination
Gene Reassortment

Question 23

What are spontaneous mutations?

Answer 23

Mistakes made during genome replication

RNA viruses higher rate of mutation (enzymes cannot proofread)
10 000 bp RNA virus - average 1 mutation per new genome

	cf. DNA viruses mutation rate – 1 in 108 nucleotides

Very high replication rate of some RNA viruses means very large numbers of mutant viruses (e.g. HIV 109 viruses/day)

Question 24

What is meant by gene transfer between viruses?

Answer 24

Transfer of genetic information between two, usually related, viruses which have infected the same cell

Production of hybrid genomes
– entire gene(s)/gene segments derived from another virus

Mechanisms

Recombination
Reassortment (segmented viruses)
Viruses (/or cell)

Question 25

What is recombination?

Answer 25

Relatively rare: occurs between viruses with related DNA/RNA sequence or

Between virus and host nucleic acid

Can lead to viruses acquiring host sequences

Question 26

What is meant y gene reassortment?

Answer 26

Can occur for viruses with a segmented genome

Simple exchange of genes can occur when two different viruses infect a cell
e.g. influenza, rotaviruses

Rapid evolution of virus variants
Can combine with other viruses and change apart of its gnome making it more resistant to immune system

Question 27

What are the consequences of viral mutations?

Answer 27

Lethal mutation, silent mutation, growth advantage/disadvantage

Circumstances which limit the ability of the virus to persist (e.g. immune response) , favour emergence of mutants which are better equipped for survival