1. ALL SORTS OF STRATEGIES
RNA VIRUSES
ALL SORTS OF STRATEGIES

2. RNA Viruses
All synthesize through a double stranded intermediate - RI - replication intermediate
RNA dependent RNA polymerase of viral origin but may need host factors
Termini contain recognition signals for replicase

3. Positive strand viruses
Begin with translation to produce replicase
Makes more positive than negative strand
Limiting factor or rapid packaging so can’t act as template
Poliovirus uses VPg linked to nucleotides as “primer” - like Ad

4. 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

5. 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

6. Transcription challenges
Less temporal control than in DNA viruses
Monogenic problem
Segmented genomes usually have individual genes
Polyprotein cleavage
What would expect to see on gel in early stages of infection? As infection progresses?
What if you performed a pulse-chase experiment?

7. Synthesize own cap (Reo in cytoplasm)
Translation challenges: Recognition by ribosomes and competition from host
Synthesize own cap (Reo in cytoplasm)
Steal from host (Influenza in nucleus)
Use host enzymes
IRES

8. Transcription strategies: Togaviruses
NS at 5’ end - S at 3’
In vitro only synthesize NS proteins; stop signal leads to polyprotein
In vivo get shorter mRNA only after minus strand synthesis that codes for S polyprotein
Internal transcription site on minus strand
Minus is template for mRNA and for genome
S message is more abundant than NS as genome gets packaged

9. Coronaviruses: frame-shifts and subgenomic RNAs
Genome translated into replicase
Antigenome produced
Subgenomic mRNAs represent a nested set of RNAs - all share short 5’ sequence and a 7 base sequence but have unique AUG site and share 3’ end of genome
May be produced by jumping polymerase - 7 base sequence in various parts of genome
Get recombinant viruses with mixed infections
DI particles are common

10. Influenza virus - segmented negative strand antigenic drift (mutations) vs shift (reassortment)

11. Influenza - negative strand virus
Replication in nucleus using viral enzymes but need host RNA-P to function
Virion enzyme cleaves cap from host mRNA and uses it to extend; adds poly A tail

12. One gene per segment except for two segments producing spliced mRNAs in two different reading frames yielding two proteins

13. 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

14. 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

16. Retroviruses: diploid ssRNA with repeats at ends
RT needs a primer - uses tRNA at primer binding site
Synthesized to end and jumps to 3’ end of strand
Uses PPT as template for second strand
Makes another jump
Results in dsDNA with Long Terminal Repeats
Needed for integration
Contains promotor and regulatory regions
Poly A site

17. Transcription occurs after integration
Uses host RNA-P
May require host factors to enhance (cell tropism)
Polyprotein and splicing strategies

18. 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

19. 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