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Summary Virology
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Resume of the theory given in the lessons of Virology. In case figures from handbooks were used, information of the handbook is also added!
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AN INTRODUCTION TO VIROLOGYWHAT ARE VIRUSES
Viruses are the smallest, simplest & most abundant form of life on Earth
Can infect all forms of life (plants, animals, eukaryotes, bacteria)
Virion: complete, infectious virus particle
Genetic material: DNA or RNA, ss or ds
o Enclosed in protein coat (= capsid)
Sometimes lipid membrane (= envelope)
Viral genome:
o 2 core modules
Structural proteins Virion formation (building blocks)
Non-structural proteins Genome replication
o Encode for:
Capsid protein
Receptor-binding protein
Viral polymerase
o Doesn’t encode for:
Protein synthesis machinery
Proteins for membrane synthesis
No centromeres or telomeres in standard host chromosomes
Diameter: 20 – 500 nm
High abundance, but low relative biomass
Visualizing: electron microscope
Viruses are obligatory parasites (= can only function after replication in a host cell)
Depend on host cell for:
Energy production:
o Mostly ATP, by photosynthesis or metabolism of sugars..
Protein synthesis
o Ribosomes, transfer RNAs, specific enzymes
o Host ribosomes translate mRNA made by virus
Reproduction
o Host cell provides building blocks
Revolution
Viruses are important disease-causing agents
HIV, Hepatitis, Influenza…
!!! Not all viruses make us sick
Most are passengers through our body
Immune system deals w/ (some) viruses
Viruses have high genome evolution rates
Evolve rapidly
Higher mutation rate than eukaryotes & bacteria
Corona virus has largest RNA genome as we
known for so far
Viruses must be excluded from the tree of life, because:
Not alive
No ancestral viral lineages
No structure derived from a common ancestor
1
,ORIGIN OF VIRUSES
Primordial virus world or viral early hypothesis
= viruses are direct descendants of the first replicons that existed
during the pre-cellular stage of the evolution of life
Viruses existed before cells
Go very far in evolution, are very ancient
Reductive virus origin
= viruses are the ultimate products of degeneration of ancestral cells
that lost their autonomy & transitioned to obligate intracellular parasitism
Cells before viruses
Escaped genes hypothesis
= viruses evolved on multiple, independent occasions in different cellular
organisms from host genes that acquired the capacity for autonomous,
selfish replication and infectivity
Specific genes split off in particles and evolve to viruses
CLASSIFICATION OF VIRUSES: BALTIMORE CLASSIFICATION
Based on the following principles:
Nature, strandedness, orientation
& topology of nucleic acids
Nucleotide sequence
Symmetry of the capsid
Presence of an envelope
Virion & capsid dimensions
DNA GENOMES VERSUS RNA GENOMES
DNA genomes RNA genomes
Genetic material is based on DNA Genetic material is based on RNA
Most replicate in the nucleus A lot of diversity:
Use host’s DNA- & RNA-synthesizing + RNA-processing ss or ds
machinery (+) or (-)
Dominant in prokaryotes Linear of segmented
Classes 1 & 2 of Baltimore system Most replicate in cytoplasm
Genome have to encode RNA-dependent RNA
polymerase (RdRp) (cells don’t have this)
Produces RNA genomes & mRNA from RNA
templates
Dominant in eukaryotes
Classes III – VII in Baltimore system
2
,CLASSES OF BALTIMORE CLASSIFICATION
Class Features Examples Replication
I Wide variety in genome size Adenovirus Nucleus
(gapped) dsDNA
Have unfragmented genomes Herpes virus DNA DNA
genomes
Circular or linear DNA
No infection of plants
II Very small & have few genes Parvovirus Nucleus
ssDNA genomes
Replication in nucleus DNA DNA
Circular genomes (dsDNA
Specific enzyme holding intermediate)
III Mostly fragmented Rotavirus A Cytoplasm
dsRNA genomes
1 gene encodes for 1 RNA RNA
protein
All have icosahedral capsid
symmetry
IV Most plant & many Corona virus Cytoplasm
ss(+)RNA genomes
vertebrate viruses Yellow fever virus (+)RNA (-)RNA
All linear genomes Poliovirus
Small: non- Hepatitis A virus
enveloped
Larger: enveloped
Larger & many plant RNA
viruses have helical capsids
V Helical nucleocapsids Ebola virus Cytoplasm/nucleus
ss(-)RNA genomes
Some are fragmented Rabies virus RNA RNA
Not found yet in prokaryotes Influenza A virus
Linked to the most Measles virus
widespread & deadly diseases
VI Integrated parts of dsDNA in HIV Cytoplasm
ss(+)RNA genomes w/
genome of host RNA DNA
DNA intermediate
VII Not originally identified by Hepatitis B virus Nucleus &
dsDNA genomes w/ RNA
Baltimore cytoplasm
intermediate
Gapped dsDNA genomes DNA RNA and
Gaps are filled by then RNA DNA
reverse transcriptase
& genome is copied
into RNA
intermediate
THE VIROLOGY TOOLBOX
STEP 1: VIRUS ISOLATION & PROPAGATION
Susceptible cell: functional receptor may or may not be competent to support viral replication
Resistant cell: no functional receptor “
Permissive cell: capacity to replicate virus may or may not be susceptible
Susceptible & permissive cell: can take up & replicate the virus particle for sure
Infection of cells depends on the random collision of virus particles w/ cells
not all susceptible cells are infected when virus is added
!!! Not all virus particles are infectious
particle-to-PFU ratio = (# physical viral particles)/(# infectious viral particles)
Multiplicity of infection (MOI): the number of infectious particles added per cell
MOI = PFU/(number of cells)
Example: MOI = 10 adding 107 virus particles per 106 cells
STEP 2: VIRUS DETERMINATION
3
, PLAQUE ASSAY (QUANTITIVE)
Method:
1. Inoculation of bacteria on nutrient agar in Petri dish
2. Dilutions of a phage suspension
(virus stock, concentration unknown)
3. Add 0,1 ml of dilution to Petri dish
4. Count lysis area = plaque
o Phage binds to bacterial cell
cell releases progeny phage particles
taken up by neighboring cells + replicated
lysis of the cells in a circular area surrounding the original infected cell
1 plaque = 1 infectious virus particle
HEMAGGLUTINATION (PHYSICAL)
Principle: sialic acid receptors on red blood cells bind to hemagglutinin glycoproteins found on the surface of several viruses
Advantages:
Simple
Inexpensive
Limitations:
Controlling incubation times
RBC type & virus concentration
Interfering factors in the sample
(pH, T, buffer composition)
Qualified personal required
ELECTRON MICROSCOPY (PHYSICAL)
Most recently: cryo-EM
VIRAL ENZYME ACTIVITY (PHYSICAL)
Principle:
Reverse transcriptase (RT) is used
to synthesize a labeled DNA strand
DNA labeling can be done w/ radiolabeled
or fluorescently labeled nucleotides
Labeled DNA can be quantified & the amount
is proportional to the RT activity in the sample
SEROLOGY (PHYSICAL)
= Indirect Immuno Fluorescense Test
Direct: viral antigen/protein detection
Indirect: antiviral antibody detection
NUCLEIC ACID DETECTION (PHYSICAL)
= viral genome detection by PCR
VIRUS STRUCTURES
From big to small:
Virion: infectious virus particle
Envelope: lipid bilayer derived from host cell (sometimes)
Nucleocapsid: protein/nucleic acid aggregates within the capsid
Capsid: protein shell surrounding the genome
Structural unit: unit from which (nucleo)capsids are build, can contain >1 subunits
Subunit: single folded polypeptide chain
Functions of structural proteins:
Protection fragile viral genome
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