Genetic Variation in Viruses

Question 1

What are the 4 types of RNA?

Answer 1

double stranded RNA
Single stranded negative sense RNA
Single stranded positive sense RNA
retroviruses

Question 2

Only this type of viral RNA can be translated to viral protein.

Answer 2

single stranded positive sense RNA

Question 3

What are examples of double stranded DNA viruses?

Answer 3

bacteriophage, papovavirus, adenovirus, herpes viruses

Question 4

DNA-dependent DNA polymerase is used for?

Answer 4

replication of DNA

Question 5

RNA-dependent DNA polymerase is used in what type of viruses?

Answer 5

retroviruses

Question 6

DNA-dependent RNA polymerase is used for?

Answer 6

transcription

Question 7

What is transcription in negative sense RNA viruses and what enzyme is used?

Answer 7

negative sense viral RNA is converted to positive sense RNA to be translated to make viral proteins

RNA-dependent RNA polymerase

Question 8

What are examples of negative sense viral RNA?

Answer 8

orthomyxoviruses (influenza), paramyxoviruses, and rhabdoviruses

Question 9

Picornaviruses, togaviruses, and coronaviruses are what kind of RNA viruses?

Answer 9

positive sense RNA

Question 10

What is the advantage of positive sense RNA viruses over negative sense RNA viruses?

Answer 10

they can replicate and produce viral proteins much faster as they are already positive sense AKA mRNA that is ready to be transcribed

Question 11

Picornaviruses, togaviruses, coronaviruses, and retroviruses are what kind of RNA viruses?

Answer 11

positive sense RNA

Question 12

What is the only type of viruses can make DNA from RNA?

Answer 12

retroviruses

Question 13

What is the only type of viruses can make DNA from RNA? What is this process called? what are examples of viruses that do this?

Answer 13

retroviruses

Reverse transcription

HIV-1, HTLV-1

Question 14

We cannot integrate RNA into our genome. We can only integrate what type of genome into our genome?

Answer 14

double stranded DNA

Question 15

Which viruses, DNA or RNA are more easily mutated and why?

Answer 15

RNA viruses are much easier to be mutated than DNA viruses because during replication they use RNA-dependent RNA polymerase which has no proof-reading capabilities. DNA replication uses DNA-dependent DNA polymerase which has proof-reading capabilities.

Question 16

Humans have 3 types of RNA polymerases which are? What are their respective functions?

Answer 16

RNA poly I: rRNA
RNA poly II: mRNA
RNA poly III: tRNA and 5sRNA

Question 17

For humans, what is the only single stranded viral DNA?

Answer 17

Parvovirus: B19

Question 18

In dsDNA only one strand is encoded. In dsRNA both strands can be encoded. This is why RNA viruses are the only ones to engage in this type of recombination.

Answer 18

copy-choice recombination where the polymerase switches the template while copying the RNA

Question 19

Retroviruses not only produce DNA but they can also produce RNA. True or false?

Answer 19

True

Question 20

Complementation occurs between two or more mutations in __________genes, thus a ____-phenotype occurs. Non-complementation mutations occur in the _______gene.

Answer 20

different
WT
same

Question 21

Humans do not have reverse transcriptase. This enzyme is very specific for?

Answer 21

retroviruses

Question 22

Retroviruses have what sense of single stranded RNA?

Answer 22

positive

Question 23

What causes viral genetic variations?

Answer 23

spontaneous genetic variations and mutations that are induced by physical or chemical means

Question 24

Consequences of viral genetic variations can result in phenotypic changes such as?

Answer 24

-conditional lethal mutants
 e.g. temperature sensitive (ts) mutants that will grow at low temperature e.g. 31 degrees C but not at e.g. 39 degrees C, wild type grows at 31 and 39 degrees C.

• Plaque size
 that may be larger or smaller than in the wild type virus
• Drug resistance
: development of antiviral agents
• “Hot” mutants
These grow better at elevated temperatures than the wild type virus.
• Attenuated mutants
Many viral mutants cause much milder symptoms (or no symptoms) compared to the parental virus
• Enzyme-deficient mutants
Some viral enzymes are not always essential and so we can isolate viable enzyme-deficient mutants; e.g. herpes simplex virus TK

Question 25

Hepatitis B virus can only infect liver cells. What does this say about the specificity of the viral interaction with cells?

Answer 25

viral interaction with cells are very specific!! You can never use HMCV to infect mouse and you cannot use mouse MCV to infect humans. Zika virus on the other hand can infect humans, monkey, and mosquitoes (this is how viruses can circulate from animals and humans).

Question 26

What is a viral plaque?

Answer 26

A viral plaque is a visible structure formed within a cell culture, such as bacterial cultures within some nutrient medium. The bacteriophage viruses replicate and spread, thus generating regions of cell destructions known as plaques. Counting the number of plaques can be used as a method of virus quantification.

Question 27

HIV patients have to take drug for LIFE because of what resultant phenotype due to viral mutations?

Answer 27

drug resistance HIV patients have to take medications for LIFE or they will have AIDS because of drug resistance of the virus.

Question 28

What is a mutation in virus?

Answer 28

if it occurs in the coding sequence, the mu

Question 29

What is a mutation in virus?

Answer 29

if it occurs in the coding sequence (the open reading frame), the mutation consequence can be silent, missense or nonsense

Question 30

What is a selection in virus?

Answer 30

if you put the virus into very specific conditions, only part of the virus can grow and that virus is selected a condition-driven variation, causing a conditional grow of the mutant

Question 31

What is complementation in viruses?

Answer 31

it occurs when two different viruses infect one cell; if they both have different mutations they can complement each other occurs between two or more different mutations

Question 32

What is recombination in viruses?

Answer 32

mostly happen when exists homologous DNA or RNA sequences between two unrelated DNAs or RNAs

Question 33

What is reassortment in viruses?

Answer 33

very important for the influenza virus; if the viral genome has more than one segment this occurs very often rearrangement of segments genome between two or more viruses

Question 34

If you add or delete 3, 6, or 9 base pairs you will not have an ORF shift. If you add or delete 1 or 2 you have an ORF shift. True or false?

Answer 34

True | each amino acids is encoded by 3 bases called a codon

Question 35

What is the difference between silent, missense, and nonsense mutation?

Answer 35

- silent: the mutation has no effect on the gene products - missense: usually point mutation, the amino acid will be changed - -nonsense: causing big truncation or premature stop codon or OFR (open reading frame) shift

Question 36

When you reculture viruses in some certain condition, for example under temperature changes. Some viruses will not survive but others will. The ones that survive will be selected and recultured to produce new generation which will again be selected upon for viable progeny. This is?

Answer 36

selection

Question 37

CRISPR-Cas9 was adapted from a naturally occurring genome editing system in bacteria. Break and rejoin system AKA what only occurs in DNA or RNAs that produce DNA such as retroviruses?

Answer 37

recombination Exchange of genetic information between 2 genomes, classic recombination involves breaking of covalent bonds within nucleic acid, exchange of genetic information, and reforming of covalent bonds 2. This kind of break/join recombination is common in DNA viruses or the RNA viruses which have a DNA phase (retroviruses). The host has recombination system for DNA. 3. Recombination of this kind is rare in RNA viruses. 4. “Copy choice” kind of mechanism: polymerase switches the templates while copying the RNA 5. So far, there is no evidence for recombination in the negative stranded RNA viruses to cause viable viruses

Question 38

Reassortment occurs in viruses that have more than one segment. What are examples of such viruses?

Answer 38

Orthomyxovirus: Influenza virus Retrovirus: HIV, HTLV Arenavirus: lymphocytic choriomeningitis virus Bunyavirus: California encephalitis virus, hantavirus Reovirus: rotavirus

Question 39

Influenza virus and HIV have how many segments respectively?

Answer 39

Influenza virus: 8 segments | HIV: 2 segments

Question 40

What is the difference between genotype and phenotype?

Answer 40

Genotype: refers to actual genetic change from wild-type in a particular DNA or RNA sequence; Phenotype: refers to the manifestation of the genotype (phenotype = the observed properties of an organism) One genotype can have more than one phenotype.

Question 41

What is the differences between viruses and other organisms?

Answer 41

Genetic materials: RNA, ssDNA, or dsDNA Dependent on host Viruses grow rapidly --> large number of progeny virions per cell --> more chances of mutations over a short time.

Question 42

Reassortment can only occur between influenza viruses of the same type. So influenza A cannot exchange genetic material with influenza B or C.

Answer 42

This is not fully understood.