Lecture 4

Question 1

Independent entities hypothesis

Answer 1

-Evolution on course parallel to that of cellular organisms
-Evolved from primitive, pre-biotic self-replicating molecules

Question 2

Regressive Evolution

Answer 2

-Viruses degenerated from previously independent life forms
-Lost many functions
-Retain only what they needed for parasitic lifestyle

Question 3

Cellular origins

Answer 3

-Viruses derived from subcellular functional assemblies of macromolecules that gained the capacity to move from cell to cell.

Question 3

Co-evolution with host

Advantages, Disadvantages, and Characteristics

Answer 3

-Advantage: Prosperous host means prosperous virus
-Disadvantage: Virus shares same fate as host. Genetic bottleneck events can be fatal
-Typically used by DNA viruses
-Association of a given viral genome sequence with a particular host group or demographic
-Can be used to trace human origins

Question 4

Two general pathways for virus evolution

Needs Host

Answer 4

Infection of multiple host species & Co-evolution with host

Question 5

Relationships between viral co-evolution & fitness

Answer 5

-Highly virulent virus will kill the host too soon
-A virus that is too exposed will cause host to kill it

Question 5

Infection of multiple host species

Advantage, Disadvantage, and where it is usually found

Answer 5

-Advantage: If one host species is compromised, virus can replicate in another
-Disadvantage: Cannot optimize for any one situation
-Typically used by RNA viruses

Question 6

Mechanisms for viral evolution

Answer 6

-Mutations made by polymerase & other sources
-Recombination
-Reassortment
-High level of replication in infected host

Question 6

Yeast Killer Virus example

Answer 6

-L-A is a metabolic parasite of host
-M is a parasite of L-a
-M confers a selective advantage on host by encoding a toxin
-Host tolerates L-A to maintain M
-L-A tolerates M to stay in good graces with host

Question 7

Recombination

Where it is found

Answer 7

All (+) sense RNA viruses and DNA viruses
-Not much in (-) sense RNA viruses

Question 7

Mutations made by polymerase and other sources

Answer 7

All viruses but greater with RNA viruses

Question 8

Relationship of mutation and evolution

Answer 8

-Evolution requires mutation
-Mutations occur when nucleic acids are copied
-Error rate of human DNA polymerase is ~10^-9
-Virus RNA and DNA polymerases are much more error prone (around 4-6 fold)

Question 9

Reassortment

Answer 9

Only segmented viruses

Question 10

Quasispecies

Answer 10

Virus populations as dynamic distributions of nonidentical but related replicons

Question 10

High level of replication in infected host

Answer 10

Present in all viruses

Question 11

Recombination general principles

Answer 11

-Occurs when 2 genetically-distinct viruses co-infect the same cell and interact to generate progeny genomes containing genetic information from both parental viruses

Question 12

Recombination in DNA viruses

Answer 12

Break-rejoining mechanism that can occur between homologous or non-homologous sequences

Question 13

Affects of recombination

On host-virus interactions

Answer 13

Important impact on host tropism, pathogenesis, evasion of immune response, etc.

Question 14

Site specific recombination

Answer 14

-Requires special proteins that recognize specific DNA sequences to promote recombination
-Used by some viruses to integrate into the host chromosome

Question 15

Homologous recomination

Answer 15

Exchange of genetic information between any pair of related DNA sequences

Question 16

Recombination in RNA viruses

Answer 16

Template switching between replication. Viral polymerase disassociates with nascent genome and re-associates with another parental genome (Switch driven by homology between 2 RNA strands so RNA made on one strand can bind to a homologous region on a second)

Question 17

Consequence of retrovirus recombination

Answer 17

If 2 copies are genetically distinct, then recombination during reverse transcription of the (+) ssRNA genome into dsDNA can generate a new virus

Question 18

Antigenetic Drift

Answer 18

Slow accumulation of mutations in a population. Due to copying errors and immune selection

Question 19

Antigenetic Shift

Answer 19

A major genetic change caused by recombination or reassortment of genomes

Question 20

Genetic Drift

Answer 20

Change in frequency of an existing gene variant in the population due to random chance

Question 21

Founder effect

Answer 21

Reduction in genetic variation that results when a small subset of a large population is used to establish a new colony

Question 22

Bottleneck

Answer 22

Extreme selective pressure on a small population. Results in loss of diversity and accumulation of non-selected mutations

Question 23

Fitness

Answer 23

Replicative adaptability of an organism to its environment

Question 24

Why viral populations maintain stable master or consensus sequences

Answer 24

Diversity limited to ability to function within certain constraints such as…
-Particle geometry
-Genomes composed of nucleic acids limits solutions to replication of decoding of viral information
-Requirement for interactions with host cell geometry
-Requirements for interactions within the host organism