Mechanism of translation initiation in which ribosomes physically bypass, or shunt over, parts of the 5’ UTR to reach the initiation codon. When translation initiation factors are scarce, the ribosome is directly translocated from the upstream initiation complex to the start codon (AUG) without the need for eIF4A helicase activity to unwind RNA secondary structure- Adenovirus, Cauliflower mosaic virus

1. Replication of RNA viruses
Dr Vikramaditya Upmanyu
Scientist
Division of Biological
Standardization

2. Class-4
Ss +
sense
Picorn
Flavi
Toga
Calci
Astro
corona
Arteri
Class-6
Retro
Class-3
Reo, Birna
mRNA
Class-5
Arena, Bunya
Class-5
ss -
sense
Ortho
Para
Rhabdo
Filo
Borna
Bunya
dsDNA
Virion RdRp
Virion RdRp
Genome act as mRNA
Virion RdRp
Cell RNA poly
Mechanism of transcription
David Baltimore classify all viruses in six group
Class-1-Ds DNA
Class-2- SS DNA

3. Picorna and flaviviruses
Genomic RNA
Polyprotein precurssor
Structural &
nonstructural protein
1
2
3
Antigenomic
RNA
Replicating enzymes
4
5
Entry & uncoating
Translation of
genomic RNA
Proteolytic
processing
Virus
assembly
Progeny virus
RNA replication

4. Rhabdo, Filo, Borna, Paramyxo, & Othromyxo
Genomic ssRNA in nucleocapsid
Viral mRNA
Structural &
nonstructural protein
1
2
3
Antigenomic
ssRNA in
nucleocapsid
Nucleocapsid protein
& replicating enzymes
4
5
Entry & partial uncoating
Transcription
of genomic
RNA
Protein syn &
processing
Virus
assembly
Progeny virus
RNA replication

5. Astro, calci, toga, corona & ateriviruses
Genomic RNA
Nonstructural polyprotein
precurssor
nonstructural protein
1
2
3
Antigenomic RNA
Replicating enzymes
4
5
Entry & uncoating
Translation of
genomic RNA
Proteolytic
processing
Virus assembly
Progeny virus
RNA replication
Structural protein
Subgenomic
mRNA
Structural polyprotein precussors
Proteolytic
processing
and Post tranl
modification
7
8
10
9
6
11
Translation of
subgenomic
mRNA
RNA
transcription

6. Reo & Birnaviruses
Genomic dsRNAs in subviral particles
Viral mRNA
Structural &
nonstructural protein
1
2
3
Viral mRNA in subviral particles
4
5
Entry & partial uncoating
Transcription of
genomic RNA
Protein synthesis
Virus
assembly
Progeny virus
Negative strand
RNA synthesis
8
7
6
Progeny
subviral
particle
9

7. Astro, calci, toga, corona & ateriviruses
Genomic RNA
Nonstructural polyprotein precurssor
nonstructural protein
1
2
3
Antigenomic RNA
Replicating enzymes
4
5
Entry & uncoating
Translation of
genomic RNA
Proteolytic
processing
Virus assembly
Progeny virus
RNA replication
Structural protein
Subgenomic
mRNA
Structural polyprotein precussors
Proteolytic
processing
and Post tranl
modification
7
8
10
9
6
11
Translation of
subgenomic
mRNA
RNA
transcription

8. Retrovirus
Genomic RNA
1
Antigenomic
ssDNA
Unspiced viral RNA
2
Entry & partial
uncoating
Virus
assembly
Progeny
virus
dsDNA
Integrated viral
dsDNA (provirus)
4
3
Integration into host
chromosomes
DNA
replication
Reverse
transcription
5
Spliced Viral RNAs
Structural,
nonstruct &
Oncoproteins
Duplicated viral
dsDNA
Cell division
Transcription of cellular RNA poly II
6
7
7
RNA splicing
Protein
Synthesis
8
9

9. Arena and some Bunyaviruses
Genomic ssRNA in nucleocapsid
Viral mRNA for nucleocapsid protein & RdRP
Nucleocapsid protein &
RdRP
1
2
3
Antigenomic
ssRNA in
nucleocapsid 4
Entry & partial uncoating
Transcription of
half genomic RNA
Protein synthesis
Virus
assembly
Progeny virus
RNA replication
mRNA for other viral protein
Structural proteins
Transcription of
another half
antigenomic RNA
Protein synthesis
6
5
8
7
9

11. The several genes along the viral RNA are each separated by a consensus sequence that
includes termination and start signals as well as short intergenic sequences of U residues that
enable the transcriptase to generate a long poly(A) tail for each mRNA by a process of
reiterative copying (stop-start transcription, also known as stuttering). Each completed
mRNA is cleaved off, but the enzyme continues to transcribe the next gene)
Stop-start transcription (stuttering)

12. Paramyxovirus transcription also involves a process known as editing. The P gene
encodes two proteins, P and V, which share a common N-terminal amino acid
sequence but differ completely in their C-terminal sequences because of a shift in
the reading frame brought about by the insertion of two uncoded G residues into “
the RNA transcript by transcriptase stuttering
Filovirus and hepatitis deltavirus

14.  Leaky scanning- Phenomenon in which a weak initiation codon triplet on mRNA is
sometimes skipped by ribosome in translation initiation- Sendai virus , Influenza B
virus, HIV, SV40

15.  Suppression of termination (stop codon read through): Alternate
mechanism of translation to produce a protein with an extended C-
terminus- Alphavirus nsP4, reterovirus gag-pol

16.  Ribosomal Framshifting: Coronavirus orf a-orfd, Human astrovirus type I
orfIa-orfIb, reterovirus gag-pol

17. Internat ribosome entry: Picornavirus, Flavivirus

18.  Ribosomal shunting: Mechanism of translation initiation in which
ribosomes physically bypass, or shunt over, parts of the 5’ UTR to reach the
initiation codon. When translation initiation factors are scarce, the ribosome
is directly translocated from the upstream initiation complex to the start
codon (AUG) without the need for eIF4A helicase activity to unwind RNA
secondary structure- Adenovirus, Cauliflower mosaic virus

19. PREVENTION IS BETTER THAN CURE
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