Viruses Flashcards
What are viruses?
Viruses - obligate intracellular parasites
They are non-living in a traditional sense of replication, therefore they rely on the host cell for replication of their genomes and assembly of new virus particles
They are capable however, of Darwinian evolution
Most living organisms can or are infected with viruses
They are the most abundant ‘life-form’, with a viral mass equivalent to all prokaryotes
Most are bacteriophage: There are 10 ‘phage for every bacteria on earth
Why are viruses very diverse?
They are extremely diverse - over 40,000 isolated and 3,000 named
Diversity arises from:
Virus morphology - all shapes
Size - from 3 genes to >1000 genes
Infection outcome - Death, non-lethal to asymptomatic
Mode of transmission - respiratory, blood borne and faecal-oral route
Hosts - single cell, complex and multiple hosts
Disease progression - rapid and slow
Therefore it is difficult to define a virus
What are some defining properties of a virus?
- Their genomes are made of DNA or RNA
- Viruses protect their genomes with a protein coat (the repeated use of a single structural protein is common in viruses)
- Viruses can self-assemble from their components
- They must infect cells in order to multiply
- The viral genome contains all the information to build the particle and perform the entire virus life cycle
How would we be able to find a virus?
Viruses infect species in all three domains of life and all 6 kingdoms
They have been isolated from all environments: natural, man-made, aquatic, sedimentary and extreme
Most infect single-celled organisms in soil, sediment, and the open ocean
To find them:
- Look within organisms exhibiting obvious disease
- Or search for them where there is no apparent disease (either in environmental samples or new viruses in animals/insects)
How could we detect a virus we found?
In order to detect certain elements we can use:
ELISA - to detect host antibodies
PCR - detect viral genomes
Western blot - identify virus components
Direct visualisation - we can see the distinctive morphology
Due to individual virus species being not highly abundant, it becomes difficult to amplify all these viruses in cell culture as conditions will vary
This lead to virus identification techniques being developed that do not rely on cell culture amplification
What classification of viruses do we use?
Baltimore Classification
Types of Classification are based on advancements in RT/PCR, genome sequencing and reverse genetics
Class 1-7
dsDNA, ssDNA, dsRNA, (+)ssRNA via (-ssRNA), (-)ssRNA, (+)ssRNA via dsDNA and ss/dsDNA
Describe class I - double stranded DNA (dsDNA)?
This can be subdivided into two further groups
- Replication is exclusively nuclear - the replication of these viruses is relatively dependent on cellular factors
e. g. Herpesviruses - Replication occurs in the cytoplasm - the viruses have evolved the necessary transcription/replication factors of their genomes and are therefore largely independent of the cellular machinery
Describe herpes viruses?
There are two different pathologies
- Herpes simplex virus - (HSV-1) transmitted by mouth and causes cold sores
- Epstein Barr virus - (HSV-4) transmitted by saliva, responsible for infectious mononucleosis commonly known as glandular fever
The genome is 150,000 bps, which encodes for 80-90 genes
Mechanism:
Attachment to the cell surface, uncoating, entry of genome into the nucleus, replication of DNA by the viral-DdDp, transcription and export of viral mRNA, translation of viral proteins, assembly and release
Describe class IV - single stranded +sense RNA, (+)ssRNA?
This can be subdivided into two further groups
- Viruses with polycistronic mRNA meaning the genome RNA forms the mRNA, which is translated to form a polyprotein product (then cleaved into mature proteins)
- Viruses with complex transcription - two rounds of translation or sub-genomic RNAs that are necessary to produce the genomic RNA
Main properties: The genomic virus is message sense They replicate in the cytoplasm e.g. Picornaviridae These viruses are responsible for the common cold, polio and FMDV
Describe class V - (-)ssRNA and class VI - (+)ssRNA with DNA intermediate?
Class V - (-)ssRNA:
This is responsible for influenza
It has 8 segments of linear (-)sense ssRNA, not like mRNA
Class VI - (+)ssRNA with DNA intermediate:
These can be lentiviruses: HIV
What unique elements make viruses diverse?
Double/single stranded, DNA/RNA
Linear/Circular
Segmented/Non-segmented
+ or - sense
What are capsid proteins?
Usually highly positively charged (basic) proteins - rich in arginine and lysine Role - to package nucleic acid
They have nucleic acid binding proteins (specific and nonspecific interactions)
They self assemble
Non-enveloped viruses - poliovirus
What are icosahedral viruses?
They are genome protection vehicles
The helical arrangement allowed symmetry and strength
However, the viral nucleic acid alone can be infectious
How are the genomes protected in icosahedral viruses?
They have a matrix, lipid bilayer and an envelop glycoprotein surrounding the capsid and the genome
Enveloped viruses - HIV, herpes simplex
What are triangulation numbers associated with icosahedral viruses?
Many viruses are based on icosahedral symmetry - 20 sides
Each side can be split into 3 - giving multiple copies of one or more proteins
Therefore 60 subunits
T = 1 (one side that is split into 3)
But trying to subdivide any further can break symmetry
Not all proteins are in equivalent positions: pentamers and hexamers
You need a five and six-fold particle axes to make it work
