RNA virus

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RNA VIRUSES

ALL SORTS OF STRATEGIES

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RNA Viruses All synthesize through

a double strandedintermediate - RI -replicationintermediate

RNA dependent RNApolymerase of viralorigin but may needhost factors

Termini containrecognition signals forreplicase

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Positive strand viruses

Begin with translation to

produce replicase

Makes more positive than

negative strand

Limiting factor or rapid

packaging so cant act

as template

Poliovirus uses VPg

linked to nucleotides as

primer - like Ad

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Negative Strand Viruses

Contain enzymes for transcription in virion

Make mRNA prior to antigenome

Message gets capped; genome does not

Plus strand is template for minus strand genome

Makes more minus than plus strand

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dsRNA viruses - conservative

replication Uncoating activates

enzymes that produce

mRNA

+ RNA also gets packaged

Then complementary -

RNA is produced

No dsRNA free in cell

Protects against IF

induction

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Transcription challenges Less temporal control than

in DNA viruses

Monogenic problem

Segmented genomesusually have individual

genes Polyprotein cleavage

What would expect to seeon gel in early stages ofinfection? As infection

progresses?

What if you performed apulse-chase experiment?

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Translationchallenges: Recognition by ribosomes

and competition from host

Synthesize own cap

(Reo in cytoplasm)

Steal from host

(Influenza in

nucleus)

Use host enzymes

IRES

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Transcription strategies: Togaviruses

NS at 5 end - S at 3

In vitro only synthesizeNS proteins; stop signalleads to polyprotein

In vivo get shorter mRNA

only after minus strandsynthesis that codes for S

polyprotein

Internal transcription siteon minus strand

Minus is template formRNA and for genome

S message is moreabundant than NS as

genome gets packaged

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Coronaviruses: frame-shifts and subgenomic

RNAs

Genome translated intoreplicase

Antigenome produced

Subgenomic mRNAs representa nested set of RNAs - all share

short 5 sequence and a 7 basesequence but have unique AUGsite and share 3 end of genome

May be produced by jumpingpolymerase - 7 base sequence in

various parts of genome Get recombinant viruseswith mixed infections

DI particles are common

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Influenza virus - segmented negative strand

antigenic drift (mutations) vs shift (reassortment)

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Influenza - negative strand virus

Replication in nucleus

using viral enzymes butneed host RNA-P to

function

Virion enzyme cleaves

cap from host mRNA anduses it to extend; adds

poly A tail

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One gene per segment

except for two segments

producing spliced mRNAs

in two different readingframes yielding two

proteins

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Ambisense genomes

Bunyaviridae such as

Hantavirus

Genome is used to make

short positive mRNA

Genome is replicated and

antigenome (plus strand)

is used to make second

mRNA

Antigenome does not act

as message

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Nonsegmented negative strand viruses:

Mononegavirales (rhabdo, filo, paramyxo)

Hypothesis: Start-stop Template 3 end start point for

virion L (RNA_P) and goes to

termination signal and mRNA

release - then cap and poly A

added

Some polymerase reinitiates at

next initiation signal and goes

to termination; process repeats

Each subsequent RNA may be

produced at a lower frequency(20-30% less)

Replication requires N capsid

and NS proteins to read through

to complete copy

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Retroviruses: diploid ssRNA with

repeats at ends

RT needs a primer - uses tRNAat primer binding site

Synthesized to end and jumpsto 3 end of strand

Uses PPT as template forsecond strand

Makes another jump

Results in dsDNA with LongTerminal Repeats

Needed for integration

Contains promotor andregulatory regions

Poly A site

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Transcription occurs after integration

Uses host RNA-P

May require host factors

to enhance (cell tropism)

Polyprotein and splicing

strategies

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HIV is a more complex retrovirus

Transactivator protein

(TAT) needed for high

level of transcription

TAT binds to TAR RNA

and causes readthrough

beyond 5 region

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REV binds to REV Response Element

(RRE) in message Early messages are highly

spliced and produce

mainly TAT, REV and

Nef

When REV increases and

binds to message, there is

less splicing

Leads to synthesis of gag,pol, env