Evolution Flashcards
What is virus evolution?
The constant change of a viral population in the face of selection pressures
What are quasispecies?
Viral populations that exist as dynamic distributions of nonidentical but related replicons
What is lethal metagenesis?
The elevation of mutation rates by exposure to a mutagen or an error-prone polymerase to the point at which resulting population of genomes has lost fitness and is incapable of propagating
What is an error threshold?
A mathematical parameter that measures the complexity of the information that must be maintained to ensure survival of a population
What is genetic bottleneck?
A descriptive terms evoking the extreme selective pressure on small populations that results in loss of diversity; accumulation of selected mutations; or both
What is Muller’s Ratchet?
A model positing how small asexual populations decline in fitness over time if the mutation rate is high
Mutations are acquired, never removed: Rachet “clicking” relentlessly in one direction
If too many mutations occur, fitness decreases
What is genetic drift?
Diversity in viral genomes that arises as a result of errors during genome replication and immune selection
What is genetic shift?
Diversity in viral genomes that arises as a result of re-assortment of genome segments or recombination between genomes
What is a root in a phylogenetic tree?
common ancestor of ALL organisms in tree
What is a node in a phylogenetic tree?
aka internal node
Common ancestor of species; diversification of species
What are tips in a phylogenetic tree?
aka terminal nodes
current organsism
What is a sister taxa in a phylogenetic tree?
organisms that come from the same common ancestor
What is a branch in a phylogenetic tree?
the part of an evolutionary tree that connects nodes
Is the best way to read an evolutionary tree is across the tips (terminal nodes)?
NO because nodes can be rotated
In a cladogram, what matters?
Topology (branching order)
In a phylogram, what matters?
Topology and branch length
What is an easy way to find the number of clades?
Count the number of nodes
What type of influenza virus strain has the greatest capacity to cause pandemics?
Type A because they have a higher mutation rate
Small incremental increases in genetic change over type would be the result of _________
Genetic drift
Rapid increases in genetic change over time would be ________
Genetic shift
Is genetic drift analogous to natural selection?
No it is not because genetic drift is random, natural selection is survival of the fittest
What are some representations of genetic drift?
Bottleneck effect
Founder effect
What scientific discipline is Paleovirology primarily built on?
Genetics/genomics
The identification of giant viruses contributes to what type of origin of viruses theory?
Regressive model
What genetic shift caused an increase in human pandemics?
Diversity arising from reassortment of genome segments
What is the host virus-arms race in paleovirology?
Genetic conflict
Host = mostly antiviral genes (intrinsic defense)
Molecular game of “rock-paper-scissors”
- Host winning (rock) = virus wants to replicate
- Virus winning (paper) = viral evolution
- Host winning (scissors) = host evolution (host will evolve along with the virus)
What is the evolution guided functional analysis of host-virus arms races?
“Antiviral genes” from different related species
Concept: synyonymous and non-synonymous changes: dN/dS
What are orthologs?
Same gene, same function, different species
Evolved from common ancestor
What is positive selection in this analysis of host-virus arms races?
Rate of nonsynonymous changes are greater than synonymous changes
What are the three phases of the evolution guided functional analysis of host-virus arms races?
Phase 1: Analyze sequences for positive selection
Phase 2: Determine phenotypic consequences of ortholog variation
Phase 3: Map positively selected changes onto host-virus interaction
What is the transferrin receptor (TfR1)?
Opposing selective pressures balanced during evolution
- Iron uptake; essential for all cells
- Receptor for variety of viruses
A: Residue positions under positive selection (red stars; rodent TfR1)
- Rapidly evolving
- In binding sites for 2 viral families
B: Residue positions under positive selection in red (human TfR1)
Are viruses always mutating?
Yes
How do viruses evolve?
“Burst-Concept”
Single-cell infected with poliovirus = 10,000 new virus particles (8 hrs)
Interface between host defenses and viral replication provides basis for selection and evolution
How do you avoid the “rachet”?
Increase genetic diversity
Diversity of a virus population is necessary for survival
- Remove diversity and the population suffers
How can you increase genetic diversity?
Recombination
Reassortment
Mutations
What is Nextstrain?
Open source platform
Powerful analytic and visualization tools
Aid epidemiological understanding
Improve outbreak response
What is the key for a virus to enter the cell?
Spike protein
Is virulence a positive or negative trait?
Can be both
Positive as transmitting it for better
Negative as transmitting too much causes a dead end since virus will just be dead
How did SARS-CoV-2 variants of concern (VOC) arise?
Genetic mutations
- spike protein
How did SARS-CoV-2 VOC persist?
Mutations improve virulence and/or transmissibility
VOC: Increased fitness
- reproduce efficiency in host
How old are viruses?
Molecular clocks
- Identify viruses in hosts
- Herpresvirus: Arose ~million years ago
- Molecular evolution estimates of Marine retroviruses: > 450 Mya
Are there multiple origins of ssDNA viruses?
Yes
Did viruses evolve after humans arrived?
No, evolved long before humans
Have all human viruses evolved from animal viruses?
Yes
What is the assumption of the evolution of new viruses?
Assumption: New viruses can only arise from viruses that are in existence, not de novo
Viral populations often maintain consensus sequences despite opportunities for extreme variation
