viral genomes and replications
Virus replication
Genomes - Dna or RNA
Never both!!!
ssRNA
"+" single stranded RNA
Same nucleotide sequence as viral mRNA
"-" single stranded RNA
Base sequence to viral mRNA
Circular or linear
Segmented - linear RNA virus, multiple segments of molecules
Help evolve and adapt very fast
Reassortment - combination of original parental strain
Reason why flu vaccine is updated - because previous year does not protect from evolution
Viral Genomes
Size
DNA viruses - Larger
Viruses of eukaryotes - larger
Viruses that infect bacteria & archaea - double stranded DNA viruses (bacteriophages)
Nomenclature and taxonomy of viruses
Phylogenetic species concept does not apply to virus
They adapt and mutate, evolve too fast!
Only rely on Genus
-virus
Family
-viridae
Can be named based on:
Host
Morphology & structure
Naked
Enveloped
Helical or icosahedral
Genome composition
Baltimore classification
Route of transmission
Respiratory, sexual transmitted
Baltimore Classification
Based on genome composition
Class 1 & 7 - Double stranded + DNA
Class 1 - traditional transcription
Class 2 - single stranded DNA +
Synthesis minus strand
Once duplicated - minus strand discared
Intermediate form is transcribed
Class 3 - double stranded RNA +
Just transcribe minus strand
RNA dependent RNA polymerase
Class 4 - ssRNA +
Used directly as mRNA
Class 5 - ssRNA -
Transcription of minus strand
RNA dependent RNA polymerase
Class 6 - retrovirus - ssRNA +
Reverse transcription
Class 7 - reverse transcription
Produce mRNA
To replicate
Checkpoint - A newly discovered virus uses an RNA-dependent RNA polymerase and carries a negative-sense RNA genome. Which Baltimore group does it belong to?
Class 5
Bacteriophage life cycle
- T4 - lytic
Lambda - lysogenic
Complex structure
Inject DNA into host cell
Lytic cycle - adsorption / attachment to host cell
Penetration - nucleic acid is injected into the cell
Capsid never enters cell
Biosynthesis
Genome is replicated
Maturation
Phage particles assemble into bacteriophages
Release of
Checkpoint - Which of the following leads to the destruction of the host cells?
Lytic Cycle
Circular permutation - each copy of genome contains same set of genes, but arranged in a different order
Genome is replicated
Recombination -> concatemer (linked genome copies)
Endonucleases cut DNA as its packed into capsid
Lysogenic cycle - temperate phages -
Lysogeny - host chromosome carries bacteriophage DNA
Viral DNA integrates into host chromosome - Prophage
As cell divides, viral DNA also replicates
Every daughter cell carries prophage
Induction - depends on condition
Excision of prophage - cut off host DNA, then enters Lytic cycle
ANIMAL virus life cycle
enveloped majority - glycoprotein spikes bind to membrane receptor (membrane fusion)
Adsorption - attachment to host cell receptor
Specific host range,
cell specific (tropism)
Entry
Membrane Fusion (picture)
Receptor mediated endocytosis (picture)
uncoating (release of nucleic acid from capsid of virus)
Once DNA is in cytosol
Virus can complete all life cycle phases
Need to be transported into Nucleus (DNA polymerase location)
Once genome is inside of cell
Replication , synthesis of protein
DNA - travel into nucleus
RNA - complete replica and synth in cytoplasm
Maturation / assembly
Mature virus particles construct (assemble)
Viral spikes are inserted into host cell membranes- origin of membrane from host
When it comes out, virus contains spikes from membrane
Release of mature virions
Lysis - rupture
Exit via exocytosis
Checkpoint -
Infection Outcomes (primarily animal)
Acute Lysis virus infection
Common cold, flu
Infected
Sudden increase of virions
Immune system kills virus
Oncogenic
Promotes Tumor-inducing viruses
Transform cell into cancerous cell
Type of infections
Latent virus infection
Virus remains in equilibrium host cells
Then wake up
Chickenpox -> shingles
Cold sores
Remains hidden in neurons for a long period of time until activated
Persistent infection (chronic)
Occurs slow increase gradually over a long period of time
Detectable virions gradually build
HIV (10-15 years)
No symptoms, aids later time after infection
*understanding life cycle of virus - nature and outcomes
Type of disease may produce
Nature of life cycle: impact
Pathogenicity
Transmission *high copy #
Diagnosis
Treatment
Response to host immune defense
Measures to control infection
Oncovirus - cancer causing
Oncogene - Tumor inducing genes
Protein synthesis will induce formation of tumors
Tumors Characterized by Unregulated division
Ex: Papillomavirus
Epstein barr virus
Ebola - filovirus- acute
Symmetry :Helical + enveloped
Sever acute, fever = Fatal (high mortality)
Spreads sporatic
Genome : 7 genes, Linear ss (-) RNA - class V (5)
RNA dependent RNA polymerase copies into + ssRNA
Transmission - ,direct contact with bodily fluids
Blood, saliva, urine, vomit, feces
Released by budding
Flu - Orthomyxoviridae - influenzavirus - acute
Severe disease
Seasonal epidemic
Rare pandemic - spanish flu (only Spanish speak of)
Transmitted by aerosolized & fomites (door handles)
Infectious dose is very low
Killed patient before transmission ??
Structure
Icosahedral, envelope
Hemagglutinin-h1 - mediates attachment
Neuraminidase - n1 - cleaves , facilitates virion release
Ss(-) RNA class V (5)
Genetic reassortment - 2 strain infect same cell, new daughter cell has recombination of both parent strains (segmented RNA genome) leads to new strain
Reason for evolution of virus and its adaption
Why does influenza evolve so rapidly compared to many other viruses?
Segmented RNA genome
VZV - Varicella zoster virus - Herpesviridae - varicellovirus
Chicken pox
Latency - 2nd stage - shingles
Will hide in neurons - latency established- pro-virus gets activated, T cells deliver VZV through skin and cutaneous lesion
Stress / aging
Structure
Icosahedral + enveloped
Genome
Linear dsDNA type I
Transmission
highly contagious
Respiratory droplets / fluids from blisters
HIV - human immunodeficiency virus - persistent
Retrovirus
Causes AIDS (acquired immunodeficiency syndrome)
Structure
Icosahedral + envelope
Genome
2 copies of linear ss (+) RNA
Targets white blood cells - wbc fight infections
Hiv kills wbc
Class VI - reverse transcriptase
Bacteriaphage
Viruses
Genetic elements
Genome
Dna or Rna
NEVER BOTH
Obligate intracellular parasites
Bacteria,protozoa,fungi,algae
Virion - infectious virus particle
Acellular
Ultramicroscopic size
Do not satisfy requirements of life
No communication or metabolic activity
Only active when infect host cell
Inactive outside of macromolecule
Highly specific for host and attachments
Do not affect other cells
Structure - simple - protein coat + nucleic acid core
Genome - DNA or RNA - single stranded or double stranded, segmented (multiple molecules)
Replicate by taking control of host cell
Sabotage host cell material
And regulate synthesis
Never encode for enzyme in Krebs cycle, or glycolysis
Lack machinery for protein synthesis
Always rely on cell's ribosomes
Replication transcription
Specific rna/dna polymerase
Roles of viruses in ecosystem
Hypothesis
Limit host populations
Without causing extinction of host
Increase host diversity - prevent dominance
Nutrient recycling
Viral shunt
Persistent viruses - kill competitors
Herpes virus
Integrate in genome, remain persistent
Symbiosis?
Genome evolution
Gene transfer
Evolve fast - genome changes extremely fast
Protein coat
Capsid
Nucleocapsid
Envelope - membrane
Always from host cell
Only in Animal cell viruses
Lack envelope in plant/bacteria cells
Matrix protein
Required virion specific
Accessory proteins - required for activity
Retroviruses - carry reverse transcriptase
Nucleic acid (dna or rna)
Capsid - protein
Naked - nucleocapsid only
Enveloped viruses - core particle +envelope
Animal viruses
Capsid :
Individual protein - capsomers
Single or several types of capsomers
Determines shape of virus - symmetry
Rod - helical
Spheres - polyhedral/icosahedral
Helical - elongated, cylindrical morphology (hollow) surrounding nucleic acid
Naked - rigid , tightly packaged (usually infect plants
Enveloped - felxible, loosely packaged (usually infect animals
Polyhedral - three dimensional - symmetrical polygon, 20 sides and 12 evenly spaced corners
Single or multiple type of capsomers
Poliovirus
32 capsomers
Adenovirus
242 capsomers
Naked and enveloped
Viral envelope - host membrane + embedded viral proteins
Envelope (capsid(dna core)))
Cellular membrane proteins are replaced by viral proteins
Some connect envelop to capsid
Spikes - proteins modified w sugars - exposed glycoproteins
Flu virus, Neuraminidases, hemagglutinin
Range from spherical to filamentous in shape
Facilitate infection of new host
Important for cell recognition
Enveloped viruses - pleomorphic
Capsid - morphology
Protection of nucleic acid
Host cell recognition - binding and penetration
Facilitate penetration into host cell
Activation of host defenses (immune system)
Detect some proteins in capsid of viruses
Trigger alert
Checkpoint - which component is not found in all viruses?
envelope
What determines shape of virus
Structure of capsid
Matrix proteins - may be required for formation of new particle
Interphase between envelope and capsid
Accessory protein - viruses typically inactive, but may require additional proteins for infection and/or replication
Lysozymes - break down bacterial peptidoglycan until reaches membrane
Facilitate infection of host cell
Animal viruses , ex flu - have Neuraminidases - breakdown of glycoprotein in connective tissue and glycolipids of animal connective tissue
RNA dependent , copies RNA polymerase for replication
Retrovirus - reverse transcriptase, rna dependant, dna polymerase
Atypical viruses
Orthopoxvirus - small pox - poxviruses - PLEOMORPHIC
Large DNA viruses, lack capsid, covered by dense layer of lipoproteins and coarse fibrils
Additional layers of protection
Bacteriophages - COMPLEX
Polyhedral capsid heads, attach to host cell
Target bacterial
Inject nucleic acid
When they infect a cell, only nucleic acid is injected
Remaining part is out of the cell
Check point - protein subunits that surround nucleic acid of a virus, known as?
Capsomeres
Which statement of viral envelopes is correct?
They originate from host cell membranes during budding
Virus life cycle - overview
Virus must induce living host cell
Synthesizes all components to make new virion particles
Permissive host - complete replication of virus
Multiply inside host
Attachment to host cell
Penetration (entry/injection)
Synthesis of virion nucleic acid + proteins
Assembly of capsids and packaging of viral genome into virions (enclose)
Release of virions -envelope forms- lysis (bacteriophage) or budding (animal cells - bud off host cell)
Prokaryote - only nucleic acid enters cell
Plant & animal - entire virion taken up by cell
One step growth curve - determines type of infection
Virus added - no increase of virions during replication,
Reduction of number of virions due to cell infection
Until virions released from cell
Latent period
Eclipse
Viral genome and protein synthesis
Early enzyme, synthesized
Nucleic acid, replication of genome, synthesis
Protein coats , capsomers , used for formation of new virions
Maturation and rise - new virion particles assembly, packaging
Towards end, release by
Lysis - naked viruses
Kill host cell
Budding/exocytosis - enveloped viruses
Does not kill host cell
Extensive replication - exhaust host cell
Eventually dies, but not INITIALLY
Burst size - number of virions released per infected cell
Virus protein synthesis - viruses rely on host cell's ribosomes
Early proteins - soon after infection
Enzymes low quantity
Viral polymerase
Proteins shut down host transcription/translation
Late proteins - coat proteins
Structural proteins
Required for virion assembly
Check point - a virus obtains its envelope during which phase
Release phase
Virus cultivation
In vivo - Must be grown living cells
Primates, live embryos
In vitro - outside a living organism, artificial setting
Bacterial cell culture
Tissue culture cells
Cells harvested from tissue biopsy (animal/plant)
Mortal cells, divide after 50-100 generations = die
Contact inhibition - only grow on one layer, neighboring cells, stop dividing
Continuous cell lines (immortal)
Cells harvested from tumor or cancer
Immortal - divide unlimited time
Ex . Cancer cells from patient in 1950s
Detecting and counting viruses
plaque assay
Titer - number of infectious virions present per volume of fluid
Plaque assay - assay used to determine the titer
Empty spot, where cell has lysed - plaque
Plaque forming per millimeter
Virus infects host cell on monolayer
Not all viruses cause cell to lyse
Cytopathic effect (visible damage to host cell )
Viruses induces damage, alters microscopic appearance
Inclusion bodies :
Compacted masses, damaged cell organelles, nucleus and cytoplasm
Syncytium :
Multiple cells fused together, multiple nuclei
Hemagglutination assay
Clumps of erythrocytes
Causes erythrocytes to clump
Molecular tests - PCR - nucleic acid
Serological tests - rapid antigen test
Use of antibodies
Enzyme linked
Checkpoint quiz - how can we demonstrate effect of virus on host cells in vitro
Cytopathic effect in tissue & plaque assay
Viroids & prions
Infect cell, cause damage
Viroids - nucleic acid , no protein
Circular single stranded RNA naked molecules
Do not encode proteins
RNA is ribozyme - able to catalyze its own replication
No protein capsid
Depend on host - encoded enzyme for replication
Depend on Host RNA polymerase
ALL Viroids - always infect plants
Wound- enters cells
Plant cells interconnected via plasmodesmata
Growth related disease
Interferes with gene expression, can mimic small regulatory RNA - gene silencing
Check point - Which feature distinguishes viroids from viruses?
Lack capsid , composed of circular RNA
Viroids - ONLY RNA, nucleic acid, no protein
Prions - ONLY PROTEIN, no nucleic acids
Prions - no nucleic acid, only protein
Animal , yeast, pathogens - severe neurological disorders
Creutzfeldt-Jakob disease - severe!!
Transmissible by ingestion, transplant, surgical instrument
Pathology - catalyze protein conformational hanged, lead to clumping and accumulation of proteins
Two different conformation
Native cellular form
Pathogenic form
Different protein structure
Replicate by converting other proteins to conform, transmissible, convinces others via positive feedback loop.
Start aggregating - form different structures inside cell
Amyloid plaques
Check point - which describes how prions propogate?
Convert normal proteins into misfolded prion form This conversion leads to a chain reaction, where the misfolded proteins trigger other normal proteins to also adopt the abnormal structure, thereby propagating the prion disease.