Evolution of viruses Flashcards
What is the Baltimore classification?
A way of grouping viruses based on genome nucleic acid differences I - dsDNA II - ssDNA III - dsRNA IV - positive ssRNA V - negative ssRNA VI - ssRNA w/ reverse transcription step VII - dsDNA w/ reverse transcription step
What are some examples of dsDNA viruses?
Can have genomes from 5kb - 2.5Mb
Includes Herpesviridae, Poxviridae (cytoplasmic replication)
Adenoviridae (large) and papillomaviridae, polymaviridae (small)
What are some examples of ssDNA viruses?
Can have genomes from 2kb - 25kb. Replicate in the nucleus using host transcription machinery. Includes Parvoviridae.
What are some examples of dsRNA viruses?
Can have genomes 4 - 30kb. Includes Reoviridae (large) and Totiviridae (small). Have a core particle to hide genome from host immune system
What are some examples of + ssRNA viruses?
Can have genomes 2 - 32kb. Replicate in the cytoplasm, genome is the mRNA. Have an RdRp for genome replication and transcription. Includes Picornaviridae, Coronaviriae (SARS). Are diverse in eukaryotes.
What are some examples of - ssRNA viruses?
Can have genomes 11 - 25kb. Replicate in the cytoplasm (most), encode RdRp for replication and transcription which is packaged in the virion. Includes orthomyxoviridae (flu), rhabdoviridae, filoviridae.
What are some examples of retroviruses and pararetroviruses?
Can integrate into host genome and use host transcription and splicing machinery. Encode a reverse transcriptase. Includes Retroviridae and Hepadnaviridae.
Describe the types of plant viruses
Mostly + ssRNA. Do get some dsRNA and - ssRNA and pararetroviruses. Have found no retroviruses and no dsDNA viruses (apart from in algae).
How do plant viruses infect cells?
Have to get past the cell wall e.g. animal chewing on plant or an animal such as an aphid feeding. Virus needs to spread from cell to cell via plasmodesmata, so encode a movement protein. Virus can be transported as a whole or in parts.
Describe the types of bacteria viruses
Bacteriophages. Mostly dsDNA, a few ssDNA, very very few RNA viruses. They are very abundant and were used as an alternative to antibiotics in the Soviet Union. Are sprayed on meat in supermarkets. Host defence mechanisms include restriction enzymes and CRISPR/Cas9
Describe dsDNA bacteriophages
Main group is the Caudovirales which includes myoviridae, siphovirida and podovirida and tectiviridae (which is icosahedral)
How do dsDNA bacteriophages enter cells?
Recognise bacterial cell wall and inject the genome in under pressure through a protein needle. In gram negative bacteria, a lysozyme complex degrades the middle peptidoglycan.
Describe the types of viruses of Archaea
Not much known. Nearly all dsDNA, some ssDNA, no known RNA viruses. Many are not related to bacteriophages and have unusual morphologies e.g. pincers.
What are the giant viruses of amoebae?
Viruses with big genomes. Includes mimivirus which has a 1.2Mb dsDNA genome encoding 900 genes and a 0.6um particle; pandoravirus which has a 2.8Mb dsDNA genome encoding 2500 genes and a 1um particle. Have also found pithovirus from a permafrost sample which has a 0.6Mb dsDNA genome, 500 genes and a 1um particle. Size of these viruses overlap with small bacteria and some intracellular parasitic eukaryotes.
Describe virus-like entities
Have no capsid protein, is a selfish genetic element. Includes:
Satellite virus - encodes a capsid protein, needs a helper virus to replicate
Satellite nucleic acid - needs a helper virus for encapsidation and replication
Hepatitis delta virus
Viroids - circular ssRNA, doesn’t encode protein, in plants
Capsid-less viruses
Endogenous retroviruses and retrotransposons
Plasmids
Describe the hepatitis delta virus
Circular ssRNA, encodes 1 protein expressed in 2 forms by RNA editing. Needs HBV for envelope proteins and uses host RNA pol II for replication and transcription.
Describe some capsid less viruses
Mitoviruses (infect fungi mitochondria and are vertically transmitted)
Narnaviruses (infect fungi, transmitted vertically/during mating)
How do we know there is a common ancestry of RNA viruses?
All encode an RdRp, all of which have a common ancestor.
How can RNA virus phylogeny be determined?
Mostly by looking at the RdRp. In some deep branches have to use other features to resolve e.g. picorna-like helicase-VPg-protease-RdRp gene block. Get horizontal transfer sometimes - recombination with similar viruses/rare recombination with different viruses/acquisition of host genes means that virus evolution is a network rather than a tree.
What does evolutionary rate depend on?
What you are measuring. Could be mutations per site per replication, mutations between different cells in an individual, differences between individuals or differences between this years strain and last years strain.
What factors influence evolutionary rate?
Generation time, transmission (direct or vector), selection, genomic architecture, replication speed, viral enzymes (e.g. DNA repair), host enzymes, environmental effects
How can the evolution of viruses be studied beyond the previous few Myrs?
Short term substitution rates imply a common ancestor a few May. To push the timeline back, we can look at arctic samples of viruses (e.g. flu from 1918), look at introduction of yellow fever to the Americas and subsequent isolation (compare the american and african strains), look at plant viruses in permafrost
How can endogenous viral elements be used to study virus evolution?
Retroviruses integrate into the host genome (so do bornaviruses, hepadnaviruses sometimes, as well as RNA viruses if there is a co-infection encoding a reverse transcriptase and an integrase). Can be dated to before the last common ancestor if the integration is observable in many species - can work out when it occurred by comparing sequence similarity.
Describe the long term evolution of viruses
Whilst short term evolution is very fast (escaping immunity and adapting to new hosts), long term evolution is much slower due to restrictions by fundamentals. Viruses ‘cycle round in a box’ - viruses can evolve back to previous forms over generations of hosts (apart from if host antiviral evolution blocks this). Jumps in evolution are when viruses adapt to a new host (but not that different if its still a mammal, v different but v rare if not). Have found that major groups of viruses have existed in their current forms for 100s of millions of years.
What are the theories for the origins of viruses?
Reduction hypothesis (from parasitic cells losing genome) Cellular origin hypothesis (selfish genetic elements that escaped the cell) Co-evolution hypothesis (evolved alongside ancestors of LUCA in the pre and post cellular RNA-protein world)
What is the evidence for the Reduction hypothesis?
Largely discredited, apart from regarding primitive pre-LUCA photo-cells as the DNA replication enzymes are unrelated
What is the evidence for the cellular origin hypothesis?
Plausible for small viruses (picorna-like viruses, retroviruses from retrotransposons, ssDNA viruses from plasmids) as they can be traced to cellular components. However the cellular elements may be derived from a pre-LUCA ‘virosphere’ in the RNA-protein world.
What is the evidence for the co-evolution hypothesis?
Plausible for large dsDNA viruses, and for the ancestors of RNA viruses
Describe the progression from the RNA world to the DNA world
RNA world: inorganic compartments form, selfish replicating ribozymes, potential protocells
RNA-Protein world: primitive ribosomes, evolution of genetic code, RNA viruses, protocells
RNA-DNA retro world: retroviruses and reverse transcription to stable DNA. Get DNA viruses and plasmids
DNA world: bacteria and archaea and eukaryotes develop.
How did viruses have a large role in evolution of cellular life?
Evolve quickly and can evolve novel proteins (even now).
Insertion into genomes of host - retrovirus elements in many genomes
Lateral gene transfer to hosts
Co-evolution of defence mechanisms for host and virus - drove immunity and programmed cell death, may have driven cell structure, organisation, DNA genomes, eukaryotic nucleus, antiviral mechanisms repurposed e.g. RNAi, DNA and protein modification, RNA processing
Likely to be the origin of introns
What is epidemiology?
The study of the distribution and determinants of health-related states or events in specified populations, and the application of this study to the control of health problems.
What factors does epidemiology study?
Characteristics of people affected (e.g. factors that influence disease such as needle sharing)
Where cases occur
Time cases occur (short epidemic or long endemic)
Populations
Study of disease control
What are the levels of disease control
Control: reduction of transmission risks to predefined levels (e.g. bovine TB in UK)
Elimination: reduction of transmission risk to near zero (e.g. measles in USA - not present but someone could bring ini)
Eradication: reduction of transmission risk to zero (e.g. small pox)
Why is epidemiology important in disease description?
Knowledge of mode of transmission is important in understanding quarantine and containment. Need to know incubation period and period of communicability.
What is R0?
The reproduction number. Is a measure of the ability of an infection to spread throughout the population. How many cases a single case generates in a susceptible population
How does the value of R0 affect disease spread?
Needs to be bigger than 1 for infection to spread
An R0 of 1 indicates an endemic disease
The higher R0, the more difficult it is to control the disease and the younger the average age of infection.
What are some typical R0 values?
Measles is super high - 15-17
Polio is 5-6
Most (e.g. flu) are around 2
What determines R0?
Probability of transmission in a contact between infected and susceptible (can be reduced with barriers)
Frequency of contacts (depends on mode of transmission e.g. airborne/sexually transmitted) (can be reduced by staying home when ill, isolation, school closures)
Duration of infectiousness (use antiviral drugs e.g. HIV)
What is R?
R0 is for susceptible individuals only. R = R0 x proportion of susceptible individuals. Can be effected by immunisation programs and vaccines.
What is herd immunity?
Reduce risk of transmission through population by immunising some people - indirect protection.