RNA VIRUS REPLICATION STRATEGIES

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RNA VIRUS REPLICATION STRATEGIES
(excluding hepatitis delta virus/agent
replication strategy)
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RNA VIRUS STRATEGIES
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ALL ANIMAL RNA VIRUSES CODE FOR A POLYMERASE
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Need to make mRNA
PLUS (POSITIVE) SENSE RNA GENOMES
proteins
(ve) sense mRNA
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Need to make mRNA
MINUS (NEGATIVE) SENSE RNA GENOMES
proteins
(ve) sense mRNA
(-ve) sense genomic RNA
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Need to make mRNA
MINUS (NEGATIVE) SENSE RNA GENOMES RNA
polymerase must be packaged in virion.
proteins
(ve) sense mRNA
If used, RNA modifying enzymes are packaged in
virion.
(-ve) sense genomic RNA
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Need to make mRNA
DOUBLE-STRANDED RNA GENOMES
RNA polymerase must be packaged in virion.
proteins
(ve) sense mRNA
If used, RNA modifying enzymes are packaged in
virion.
Double-stranded genomic RNA
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Need to make mRNA
RETROVIRUSES
Reverse transcriptase must be packaged in virion.
DS DNA
DS DNA
VE RNA
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RNA viruses that do NOT have a DNA phase
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RETROVIRUSES
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The monocistronic mRNA problem

• Make one monocistronic mRNA per protein
• Make a primary transcript and use alternative
  splicing
• Make a large protein and then cut it into smaller
  proteins
• Include special features in the mRNA which enable
  ribosomes to bind internally

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GENOME SIZE

• TAUTOMERIZATION
• PROOF READING
• RNA VIRUSES HAVE SMALL GENOMES
• 10,000 NUCLEOTIDES
• (herpesvirus DNA 200,000)

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GENOME SIZE

• POLYMERASE
• ATTACHMENT PROTEIN
• CAPSID PROTEIN
• RELATIVELY FEW OTHER PROTEINS
• VIRION SIZE MAY BE QUITE LARGE BUT LIMITED NUMBER
  OF PROTEINS

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POSITIVE-STRANDED RNA VIRUSES

• EXAMPLES
• PICORNAVIRUSES
• TOGAVIRUSES
• FLAVIVIRUSES

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PICORNAVIRUS FAMILY (PICORNAVIRIDAE)

• SMALL
• ICOSAHEDRAL
• POSITIVE SENSE RNA
• NON-ENVELOPED

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ADSORPTION AND PENETRATION
proteins
(ve) sense mRNA
AAA
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INTERNAL RIBOSOME ENTRY SITE (IRES)
IRES
GENOMIC ( SENSE) RNA
AAAAA
VPg
start codon for translation
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Inhibition of host cell translation
Uninfected cell
Factors40S ribosomal subunit
Infected cell
Altered factors40S ribosomal subunit
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Viral translation
Uninfected cell
Factors40S ribosomal subunit
Infected cell
Altered factors40S ribosomal subunit
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RNA REPLICATION
GENOMIC ( SENSE) RNA
3
VPg
(- SENSE) RNA
VPg
3
GENOMIC ( SENSE) RNA
3
VPg
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RNA REPLICATION

• viral RNA polymerase (replicase)
• host factors also involved as accessory proteins
• new plus strands
• packaged
• templates for more replication
• templates for more translation

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ASSEMBLY
VP0, VP1, VP3
VPg-RNA enters, VP0 is cleaved
VP2, VP4, VP1, VP3
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RELEASE

• LYSIS

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NON-SEGMENTED NEGATIVE STRAND VIRUSES
Examples Rhabdovirus family (Rhabdoviridae) Par
amyxovirus family (Paramyxoviridae) Filovirus
family (Filoviridae)
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RHABDOVIRUSES
G glycoprotein SPIKES
M protein
lipid bilayer membrane
helical nucleocapsid (RNA plus N protein)
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Need to make mRNA
MINUS (NEGATIVE) SENSE RNA GENOME RNA polymerase
must be packaged in virion.
proteins
(ve) sense mRNA
RNA modifying enzymes are packaged in virion.
(-ve) sense genomic RNA
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RHABDOVIRUSES
G glycoprotein SPIKES
M protein
lipid bilayer membrane
helical nucleocapsid (RNA plus N protein)
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RHABDOVIRUSES

• EXAMPLES
• vesicular stomatitis virus (VSV)
• rabies virus

Dr FS Murphy http//www.vetnet.ucdavis.edu/fam_gra
phics/download.html
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ADSORPTION AND PENETRATION
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ADSORPTION AND PENETRATION

• CYTOPLASMIC REPLICATION
• GENOMIC RNA REMAINS IN NUCLEOCAPSID FORM

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RNA SYNTHESIS
genome (-ve)
3
5
transcription
mRNAs (ve sense)
AAA
AAA
AAA
AAA
AAA
cap
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NEW MINUS STRAND

• PACKAGED
• TEMPLATE FOR MORE REPLICATION
• TEMPLATE FOR MORE TRANSCRIPTION

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ASSEMBLY
outside cell
M protein
polymerase
inside cell
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SOME POINTS TO NOTE ABOUT RHABDOVIRUSES

• ENTIRE CYCLE OCCURS IN CYTOPLASM
• RNA POLYMERASE AND RNA MODIFICATION ENZYMES ARE
• VIRALLY CODED
• PRESENT IN THE VIRION
• THERE IS NO EARLY/LATE DIVISION

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PARAMYXOVIRUSES

• MEMBERS INCLUDE
• PARAINFLUENZA VIRUS
• MUMPS VIRUS
• MEASLES VIRUS
• RESPIRATORY SYNCYTIAL VIRUS

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PARAMYXOVIRUSES
HN/H/G glycoprotein SPIKES
pleomorphic
F glycoprotein SPIKES
helical nucleocapsid (RNA plus NP protein)
lipid bilayer membrane
polymerase complex
M protein
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PARAMYXOVIRIDAE

• PARAMYXOVIRUS SUBFAMILY
• PARAMYXOVIRUS
• RUBULAVIRUS
• MORBILLIVIRUS
• PNEUMOVIRUS SUBFAMILY
• PNEUMOVIRUS GENUS
• METAPNEUMOVIRUS GENUS

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PARAMYXOVIRUS SUBFAMILY
PNEUMOVIRUS SUBFAMILY
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hemagglutination
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HEMAGGLUTINATION

• Quick, easy, cheap
• Can use to detect virus or antibody to virus
  (hemagglutination inhibition)
• A measure of total virus particles present, not
  of infectious virus particles

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Hemadsorption - influenza virus infected cells
MURRAY, 2nd Ed., Fig 53.5
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PARAMYXOVIRUS SUBFAMILY
PNEUMOVIRUS SUBFAMILY
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Neuraminidase activity

• Destroys sialic acid/neuraminic acid

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PARAMYXOVIRUS SUBFAMILY
PNEUMOVIRUS SUBFAMILY
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PARAMYXOVIRUS SUBFAMILY
PNEUMOVIRUS SUBFAMILY
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F PROTEIN

• Fusion
• Works at physiological pH

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PENETRATION - FUSION
replicates in cytoplasm
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TRANSCRIPTION, TRANSLATION, REPLICATION
genome (-ve)
3
5
replication (protein synthesis is a
pre-requisite)
transcription
full-length copy
mRNAs (ve sense)
(ve)
AAA
AAA
5
3
AAA
AAA
AAA
(-ve)
AAA
3
5
cap
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ASSEMBLY
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ASSEMBLY
outside cell
inside cell
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ROLE OF NEURAMINIDASE
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ROLE OF NEURAMINIDASE
sialic acid
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ROLE OF NEURAMINIDASE
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ROLE OF NEURAMINIDASE
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ACTIVATION OF THE F PROTEIN
lipid membrane
CYTOPLASM
S
S
S
S
S
S
region of protein involved in fusion
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ACTIVATION OF THE F PROTEIN
endoplasmic reticulum
Golgi
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Some differences between rhabdoviruses and
paramyxoviruses
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ORTHOMYXOVIRUSES
HA - hemagglutinin
NA - neuraminidase
helical nucleocapsid (RNA and NP protein)
lipid bilayer membrane
polymerase complex
M1 protein
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ORTHOMYXOVIRUSES

• pleomorphic

http//www.uct.ac.za/depts/mmi/stannard/fluvirus.h
tml
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pleomorphic
swine flu virus - CDC
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ADSORPTION AND PENETRATION
NUCLEUS
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TRANSCRIPTION (mRNA SYNTHESIS)
cap
host cell mRNA
A
AAA
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RNA SYNTHESIS

• Endonuclease is virally coded and in the virion
• RNA polymerase is virally coded and in the virion
• Poly(A) polymerase is virally coded and in the
  virion
• Why doesnt the virus use host cell enzymes?

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RNA SPLICING
SEVERAL SEGMENTS GIVE RISE TO TRANSCRIPTS WHICH
CAN HAVE ONE OF TWO FATES
AAAAAA
AAAAAA
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RNA REPLICATION

• nuclear
• authentic copies
• replicase and transcriptase probably same enzyme
• coated with protein as made
• no clear early/late

(ve)
5
3
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ASSEMBLY

• NUCLEOCAPSIDS TRANSPORTED TO CYTOPLASM
• GLYCOPROTEINS INSERTED IN PLASMA MEMBRANE
• M PROTEINS ASSOCIATE WITH MEMBRANE
• BUD THROUGH PLASMA MEMBRANE
• HA CLEAVAGE
• ROLE OF NA

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flu HA protein and fusion
cleavage by host cell enzymes
virus
acid pH inside endosome
- conformational change, now active in membrane
fusion
Viral envelope
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NUCLEUS
Infection of next cell
HA cleavage by host cell enzymes
- HA conformational change, now active in
membrane fusion
acid pH inside endosome
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REOVIRUS FAMILY
double stranded RNA genome
outer capsid
inner capsid
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Need to make mRNA
DOUBLE-STRANDED RNA GENOMES
RNA polymerase must be packaged in virion.
proteins
(ve) sense mRNA
RNA modifying enzymes are packaged in virion.
Double-stranded genomic RNA
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REOVIRUS FAMILY
double stranded RNA genome
outer capsid
inner capsid
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ROTAVIRUS
Erskine Palmer, CDC
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REOVIRUS FAMILY

• INCLUDES
• REOVIRUSES
• ROTAVIRUSES
• IMPORTANT HUMAN PATHOGENS
• ORBIVIRUSES
• INCLUDE COLORADO TICK FEVER VIRUS

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ADSORPTION, PENETRATION, UNCOATING
Murray et al, Medical Microbiology, 2nd ed. Fig
7-5 (part)
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ADSORPTION, PENETRATION, UNCOATING

• proteases in GI tract
• attachment proteins at vertices
• cross membrane directly or via endosomes

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RELEASE

• TRANSIENTLY ENVELOPED
• BUD INTO ER AND GET ENVELOPED
• MEMBRANE IS LOST
• RELEASED BY LYSIS