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Biology 416 VIROLOGY > Evolution > Flashcards

Evolution Flashcards

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1
Q

What is virus evolution?

A

The constant change of a viral population in the face of selection pressures

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2
Q

What are quasispecies?

A

Viral populations that exist as dynamic distributions of nonidentical but related replicons

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3
Q

What is lethal metagenesis?

A

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

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4
Q

What is an error threshold?

A

A mathematical parameter that measures the complexity of the information that must be maintained to ensure survival of a population

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5
Q

What is genetic bottleneck?

A

A descriptive terms evoking the extreme selective pressure on small populations that results in loss of diversity; accumulation of selected mutations; or both

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6
Q

What is Muller’s Ratchet?

A

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

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7
Q

What is genetic drift?

A

Diversity in viral genomes that arises as a result of errors during genome replication and immune selection

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8
Q

What is genetic shift?

A

Diversity in viral genomes that arises as a result of re-assortment of genome segments or recombination between genomes

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9
Q

What is a root in a phylogenetic tree?

A

common ancestor of ALL organisms in tree

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10
Q

What is a node in a phylogenetic tree?

A

aka internal node

Common ancestor of species; diversification of species

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11
Q

What are tips in a phylogenetic tree?

A

aka terminal nodes

current organsism

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12
Q

What is a sister taxa in a phylogenetic tree?

A

organisms that come from the same common ancestor

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13
Q

What is a branch in a phylogenetic tree?

A

the part of an evolutionary tree that connects nodes

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14
Q

Is the best way to read an evolutionary tree is across the tips (terminal nodes)?

A

NO because nodes can be rotated

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15
Q

In a cladogram, what matters?

A

Topology (branching order)

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16
Q

In a phylogram, what matters?

A

Topology and branch length

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17
Q

What is an easy way to find the number of clades?

A

Count the number of nodes

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18
Q

What type of influenza virus strain has the greatest capacity to cause pandemics?

A

Type A because they have a higher mutation rate

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19
Q

Small incremental increases in genetic change over type would be the result of _________

A

Genetic drift

20
Q

Rapid increases in genetic change over time would be ________

A

Genetic shift

21
Q

Is genetic drift analogous to natural selection?

A

No it is not because genetic drift is random, natural selection is survival of the fittest

22
Q

What are some representations of genetic drift?

A

Bottleneck effect

Founder effect

23
Q

What scientific discipline is Paleovirology primarily built on?

A

Genetics/genomics

24
Q

The identification of giant viruses contributes to what type of origin of viruses theory?

A

Regressive model

25
Q

What genetic shift caused an increase in human pandemics?

A

Diversity arising from reassortment of genome segments

26
Q

What is the host virus-arms race in paleovirology?

A

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)
27
Q

What is the evolution guided functional analysis of host-virus arms races?

A

“Antiviral genes” from different related species

Concept: synyonymous and non-synonymous changes: dN/dS

28
Q

What are orthologs?

A

Same gene, same function, different species

Evolved from common ancestor

29
Q

What is positive selection in this analysis of host-virus arms races?

A

Rate of nonsynonymous changes are greater than synonymous changes

30
Q

What are the three phases of the evolution guided functional analysis of host-virus arms races?

A

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

31
Q

What is the transferrin receptor (TfR1)?

A

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)

32
Q

Are viruses always mutating?

A

Yes

33
Q

How do viruses evolve?

A

“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

34
Q

How do you avoid the “rachet”?

A

Increase genetic diversity

Diversity of a virus population is necessary for survival
- Remove diversity and the population suffers

35
Q

How can you increase genetic diversity?

A

Recombination

Reassortment

Mutations

36
Q

What is Nextstrain?

A

Open source platform

Powerful analytic and visualization tools

Aid epidemiological understanding

Improve outbreak response

37
Q

What is the key for a virus to enter the cell?

A

Spike protein

38
Q

Is virulence a positive or negative trait?

A

Can be both

Positive as transmitting it for better

Negative as transmitting too much causes a dead end since virus will just be dead

39
Q

How did SARS-CoV-2 variants of concern (VOC) arise?

A

Genetic mutations

- spike protein

40
Q

How did SARS-CoV-2 VOC persist?

A

Mutations improve virulence and/or transmissibility

VOC: Increased fitness
- reproduce efficiency in host

41
Q

How old are viruses?

A

Molecular clocks

  • Identify viruses in hosts
  • Herpresvirus: Arose ~million years ago
  • Molecular evolution estimates of Marine retroviruses: > 450 Mya
42
Q

Are there multiple origins of ssDNA viruses?

A

Yes

43
Q

Did viruses evolve after humans arrived?

A

No, evolved long before humans

44
Q

Have all human viruses evolved from animal viruses?

A

Yes

45
Q

What is the assumption of the evolution of new viruses?

A

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

Biology 416 VIROLOGY (7 decks)

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