16. Baltimore classification

Question 1

What does Baltimore classification describe

Answer 1

Viral replication strategies

Question 2

How many classes are there

Answer 2

7

Question 3

What happens to ssRNA+/mRNA

Answer 3

It synthesizes viral proteins which are then used for genome replication

Question 4

what enzymes are required for genome replication

Answer 4

RNA pol
DNA dip
DNA pol
RNA dip
In 1. and 2.=>DNA pol and dip
In 3. 4. 5.=> RNA pol and dip
In 6.7.=> RNA pol DNA dip; RNA pol RNA dip

Question 5

What are enzymes for the genesis of ssRNA+

Answer 5

FOR ALL: RNA pol DNA dip

Question 6

What are differences in transcription of replicative class 1

Answer 6

dsDNA viruses(Class I)= we have nuclear and cytoplasmic replication
Nuclear replication- viruses use cellular RNA polymerase. Transcription is regulated by cellular and viral TFs, occurring from both strands. Examples: papillomaviridae( cervical cancer) and adenoviridae(colds)
Cytoplasmic replication- viruses encode their own RNA polymerase . Ex: poxviridae(smallpox)

Question 7

What are differences in replication of replicative class 1

Answer 7

We have it for complex and simple viruses
Complex viruses- virial genome replication is mediated by viral DNA-dependent DNA polymerases
They encode proteins for the metabolism of nucleic acids.
Ex:Herpesvidirdae, poxviridae, adenoviridae
Simple viruses
-Viral genome replication is mediated by cellular DNA-dependent DNA polymerases
Ex: poliomaviridae
papillomaviridae

Question 8

What is poxviridae

Answer 8

Largest family of viruses affecting human. Ex: smallpox virus(eradicated)=> lethal disease in 30-50% of cases

Question 9

What is the ‘‘formula’’ for the first replicating class

Answer 9

dsDNA->mRNA

Question 10

What are characteristics of replicative class 2

Answer 10

ssDNA DNA viruses- they synthesize mRNA thanks to the cellular biosynthetic apparatus.

Question 11

What happens before synthesis of mRNA in replicative class 2

Answer 11

ssDNA genomes must be completed to dsDNA in order to be transcribed. The virus replicates its genome in the cell nucleus only during S phase of the cell cycle

Question 12

Who replicates viral genome in replicative class 2

Answer 12

cellular DNA polymerase

Question 13

What is the ‘‘formula’’ for replicative class 2

Answer 13

ssDNA–>dsDNA–>mRNA

Question 14

What is an example of replicative class 2

Answer 14

Parvoviridae. Parvovirus B19 causes minor disease that decreases red blood cell production. It’s small group of viruses whose DNA replication occurs in the nucleus of actively replicating cells

Question 15

What are general features of RNA viruses

Answer 15

-replication and transcription are similar processes
-must encode for RNA-dependent RNA-polymerases
-provided or synthesized quickly
-they work fast
-must provide enzymes for mRNA processing
-pass through a dsRNA intermediate

Question 16

What are characteristics of replicative class 3

Answer 16

dsRNA viruses- they have segmented genome (10-12 segments). These viruses replicate in the cytoplasm with an ssRNA intermediate

Question 17

What is replication mediated by in replicative class 3

Answer 17

Virus-encoded RNA-dependent RNA polymerase that is also essential for genome expression and its encorporated into the infectious virus

Question 18

What’s the formula for replicative class 3

Answer 18

dsRNA–>ssRNA(+)(mRNA)–> gene expression/genome replication(ssRNA-)

Question 19

What are some examples of viruses from replicative class 3

Answer 19

Reoviridae: double icosahedral capsid that can be external and internal. It belongs to rotaviruses that have gastrointestinal forms

Question 20

What are characteristics of replicative class 4

Answer 20

ssRNA(+) viruses- these genomes are said ‘‘infectious’’ as they can be immediately translated by the cellular ribosomes
While genomic RNA encodes early regulatory/replicative proteins, late proteins are encoded generated shorter/subgenomic transcriptssubsequently expressed(separation early and late)

Question 21

What happens in some cases of replicative class 4

Answer 21

Genome consisting of an ssRNA(+) is translated into a polyprotein (no early or late stages)

Question 22

Where does replicative class 4 replicates

Answer 22

In intracellular membrane(viral replication factories) rearrangements with the involvement of a viral RNA dependent RNA polymerase

Question 23

What are examples of families of replicative class 4

Answer 23

-Caliciviridae( Gastroenteritis)
-Picornavirisae(Poliovirus, Hepatitis A, Enteroviruses).They are naked viruses
-Hepeviridae(hepatits E)
-Flaviviridae( Hepatitis C)
-Matonaviridae(Rubella virus)
-Coronaviridae(Severe Acute Respiratory Syndrome SARS)

Question 24

What happens during translation and transcription of the SARS-CoV-2 Genome

Answer 24

Nonstructural proteins are synthesized from ORF1 which is broken into two separate frames. Subgenomic RNAs are formed by splicing translational signals from the 5’ genome end to the individual genes

Question 25

How does attachment and entry of SARS-CoV-2 go

Answer 25

Entry to a cell through the interaction of its spike protein with the SCE2 cellular receptor. Proteolysis by TMPRSS2 exposes a spike domain that promotes membrane fusion

Question 26

What are steps of replication and viral exit

Answer 26

1. Viral replication occurs in cytoplasmic double membrane vesicles that shelter the genome and concentrate ribonucleotide precursors 2. Structural proteins are synthesizes on the endoplasmic reticulum 3. The nucleocapsid protein in complex with positive-strand RNA genome is engulfed by membranes to form cytoplasmic vesicles 4. That exits the cell by exocytosis

Question 27

what's the ''formula'' of replicative class 4

Answer 27

(+)ssRNA-->(-)ssRNA-->mRNA

Question 28

What are characteristics of replicative class 5

Answer 28

**ssRNA(-) viruses** can be unsegmented(measles, rabies(Rhaboviridae), Ebola(Filoviridae)) and segmented genome viruses

Question 29

What's multiplication strategy of negative strand RNA viruses

Answer 29

RNA-dependent RNA polymerase enters the cell at the same time the negative-strand RNA genome enters. The genome serves as a template for synthesis of mRNA. Later in the infection, that positive strands then act as templates for replication of thenegative strand genomes

Question 30

What is the ''formula'' of replication class 5

Answer 30

(-)ssRNA-->mRNA

Question 31

What are characteristics of replicative class 6

Answer 31

**Virus A ssRNA(+) replicated through a DNA/RNA hybrid**- viruses contain a diploid RNA+ genome which, once it enters a host cell, is *reverse transcribed* into dsDNA molecule(*provirus*) which integrates into the host cell genome

Question 32

What is provirus

Answer 32

Virus that integrates into the DNA of a host cell

Question 33

What viral enzymes are involved in replicative class 6

Answer 33

Retrotranscriptase and integrase

Question 34

What happens when provirus integrates into host's genome in replicative class 6

Answer 34

It is then transcribed by the host cell's RNA polymerase II. Thus different classes of subgenomic( single and double spliced) and genomic( unspliced) are expressed

Question 35

What are some viruses from replicative class 6

Answer 35

HIV1/2- AIDS HTLV1-T-cell leukemia

Question 36

What is the ''formula'' of replicative class 6

Answer 36

(+)ssRNA--> DNA/RNA hybrid-->dsDNA-->mRNA

Question 37

What are characteristics of replicative class 7

Answer 37

**Virus A ss/ds DNA replicated through DNA/RNA hybrid**- partially double-stranded DNA viruses that replicate in the nucleus and cytoplasm of infected cells. dsDNA is completed and transcribed in the nucleus

Question 38

What can DNA from replicative class 7 generate

Answer 38

ssRNA+(cellular RNA pol II action)

Question 39

What can happen to genomic RNA in addition to being translated in replicative class 7

Answer 39

Genomic RNAs can be reverse transcribed to RNA/DNA and then ss/ds DNS which will be packed in virion

Question 40

What activity does polymerase have in replicative class 7

Answer 40

DNA, pol-RNA and -DNA dependent(reverse transcriptase) activity

Question 41

What are some examples of replicative class 7 virus

Answer 41

Hepatitis B

Question 42

What's ''formula'' to replicative class 7

Answer 42

dsDNA-->ssRNA-->mRNA

Question 43

Is DNA transient or labile

Answer 43

No

Question 44

Do DNA viruses establish persistent infections

Answer 44

Yes

Question 45

With what viral DNA genomes have to interact with

Answer 45

Host transcriptional machinery( except for poxviruses)

Question 46

Is viral gene transcription temporally regulated in DNA viruses

Answer 46

Yes. Early gene encodes DNA-binding proteins and enzymes. Late genes encode structural and other proteins

Question 47

What do DNA polymerases require to replicate a viral genome

Answer 47

A primer

Question 48

Is RNA labile and transient

Answer 48

Yes

Question 49

Can cell replicate RNA

Answer 49

No. RNA viruses must encode RNA-dependent RNA polymerase

Question 50

What does the genome structure of RNA virus determines

Answer 50

Mechanism of transcription and replication

Question 51

Are RNA viruses prone to mutation

Answer 51

Yes

Question 52

What determines how viral mRNA is generated and proteins processed

Answer 52

Genome structure and polarity

Question 53

What viruses must carry polymerases

Answer 53

All RNA viruses except for (+) RNA genome

Question 54

What viruses are always enveloped

Answer 54

(-)RNA

Question 55

What is reovirus

Answer 55

(+/-) segmented RNA genome is template for mRNA(+RNA).(+)RNA may also be encapsidated to generate (+/-) RNA and then more mRNA

Question 56

What happens in retroviruses

Answer 56

(+)retrovirus RNA genome is converted into DNA which is integrated into the host chromatin and transcribed as a cellular gene