3 - Viral Genetics Flashcards
Forms that viral genomes exist in
- DNA, RNA (mainly), DNA with short segments of RNA
- Double stranded, single stranded (+) stand, (-) strand, or ambisense
- Linear, circular, segmented, continuous, gapped
All viral genomes must encode gene products and regulatory signals required for…
- Genome replication
- Assembly and packaging of the genome
- Expression and regulatory signals
- Modulation of cell defences and propagation to other cells
Viral genomes
- Encode some, never all of the proteins required to complete viral replication
- All RNA viruses must encode either an RNA dependent RNA polymerase or a reverse transcriptase for efficient replication
- Both lack proof reading activity and contribute to viral diversity
How many replication strategies exists for all known viruses
Seven
Baltimore classification
- Based on the type of nucleic acid genome and replication strategy
- All must produce mRNA that can be translated by cellular ribosomes to produce viral structural protein
mRNA
Defined as + strand because it contains immediately translatable information
RNA dependent RNA polymerase (RdRp)
- Essential protein encoded in the genomes of all RNA containing viruses with no DNA stage
- Cells do not have ability to replicate viral RNA genomes or to synthesise mRNA from viral RNA
- VIral RdRp synthesizes mRNA which is readable by cellular ribosomes
Baltimore classification groups
- Group 1: dsDNA
- Group 2: ssDNA
- Group 3: dsRNA
- Group 4: RNA (+)
- Group 5: RNA (-)
- Group 6: RNA (+, RT)
- Group 7: dsDNA (RT)
Group 1
- +/- dsDNA
Enzymes required: - DNA-dependent DNA Polymerase (DdDp)
- DNA-dependent RNA Polymerase (DdRp)
- Viral dsDNA synthesized with DdDp
- Viral mRNA synthesized with DdRp (viral
protein translated)
Examples of group 1 viruses
- Herpesviruses
- Papillomavirus
- Polyomavirus
Group 2
- (+) ssDNA
Enzymes required for replication: - Cellular DdDp (forms +ssDNA after dsDNA)
- Cellular DdRp (forms viral mRNA)
- RNA can only be synthesized from dsDNA, complementary DNA has to be synthesised first, to convert genome to dsDNA
Uses for newly synthesized viral dsDNA
Used as template to synthesise:
- +viral mRNA: translated to viral protein
- Ss(+) viral DNA genome
Examples of group 2 viruses
Parvovirus
Group 3
- (+/-) dsRNA
- vRdRp copies dsRNA genome for packaging into new virus particles and also transcribes vmRNA
- vmRNA translated to viral protein.
Genome replication of reoviruses and birnaviruses
- Both have segmented genomes
- Genome replication is monocistronic (each gene encodes a single mRNA and a single protein)
- Replication occurs within the capsid in the cytoplasm, not in the nucleus as for DNA viruses
Example of Group 3 viruses
Rotavirus
Group 4
- (+) ssRNA
- Viral (+) RNA can act as mRNA and directly accessed by cellular ribosomes to translate viral protein
- Viral RdRp copies (+) strand to (-) complementary RNA
- (-) RNA used as template for synthesis (by viral RdRp) of (+) ssRNA for incorporation in new virus particle
Examples of group 4 viruses
- SARS-CoV-2
- Dengue virus
- Sindbis virus
- Poliovirus
Group 5
- (-)ssRNA
- (-) RNA cannot be accessed by cellular ribosomes. (+) copies ie. viral mRNA must be made first
- Viral mRNA is synthesized from (-) RNA template by vRdRp that is packaged into the virus and is ready to be used upon infection
- (-) RNA template is also used to synthesise (+)
vRNA intermediate which serves as the template for (-) vRNA for packaging into new virus particle
Example of group 5 viruses
- Influenza virus
- Measles virus
Group 6
- (+) ssRNA (RT)
- Retroviruses convert diploid (+) RNA genome to cDNA (RdDp) with the viral reverse transcriptase, that is packaged into the virion.
- (-) ssDNA acts as template for synthesis of dsDNA intermediate.
- This dsDNA is integrated into host cell chromosome with viral integrase.
- When cells are activated, viral mRNA is transcribed with cellular DdRp, then translated to viral protein.
- Packages as diploid genome (2 copies of ss(+)RNA per virion)
Group 6 example virus
HIV
Group 7
- (+/-) dsDNA (RT)
- dsDNA viruses with a gapped genome, with an RNA intermediate
- Immediately upon infection of cell, DNA gap is repaired by cellular DdDp (a covalently closed circular form of vDNA is synthesized: cccDNA)
- cccDNA is template for transcription of
viral mRNA and subgenomic/pregenomic RNA - Serves as template for the viral reverse transcriptase (RdDp) , for production of viral DNA genome
Example of group 7 virus
Hepatitis B virus
DNA directed DNA polymerases proofreading
- Proofreading capabilities in the form of exonuclease activities
- Most RNA-dependent RNA polymerases do not possess this capability (causes higher error)
- Many of these errors cause lethal amino acid changes, while other mutations may appear in the genomes of infectious virus particles
RNA viruses’ RNA-dependent RNA polymerase fidelity
Differs in how accurately they copy viral genomic RNA
Enzyme that provides proofreading function in RNA viruses
ExoN, a 3’ - 5’ exonuclease
Viral quasispecies
- RNA polymerases lack 3’ exonuclease proofreading activity
- Mutations accumulate during replication and recombination
- RT lack 3’ exonuclease activity and retroviruses mutate and evolve at rates similar to those of non RT RNA viruses
- Retroviruses also exist as quasispecies
Average error frequency of RNA polymerases
1 in 10^4 - 10^5
Most mutations are inconsequential or result in viruses which are not able to replicate. How can some mutations benefit viruses
By enabling viruses to:
- Successfully evade the immune system
- Develop drug resistance
- Thwart vaccination strategies
What does process of recombination that occurs in RNA viruses lead to
The formation of chimeric molecules
from parental genomes of mixed origin
Co infection of a cell by genetically distinct viral strains
- Leads to the generation of recombinant viruses.
- Can occur in both non-segmented viruses or within a segment of a segmented virus.
Co-infection of a cell by genetically distinct strains of a retrovirus
Leads to the generation of ‘heterozygous’ virus particles, after which a template-switching event can
lead to a recombinant provirus.
Retroviral genome
Psuedodiploid (2 RNA strands)
Why are retroviruses considered not truly diploid
Because only one allele at each locus is preserved in the integrated provirus, and any progeny produced from a cell harboring a single recombinant provirus will transmit only one allele at each locus in its progeny.
Reassortants
- If a cell is infected with two different influenza viruses, the RNAs of both viruses are copied in the nucleus
- When new virus particles are assembled at the plasma membrane, each of the 8 RNA segments may originate from either infecting virus.
- The progeny that inherit RNAs from both parents are called reassortants.
Pandemic IVA
- Express HA that has not been seen by most people before (there is no pre-existing immunity to that new virus)
- This HA may have originated in a pig (swine) or bird (avian)
HA
- Hemagglutinin
- The molecule that attaches to the receptor and against which the protective immune response is targeted
Viral diversification mechanisms
Recombination and reassortment
