Summary of virus introduction
n Two critical experiments that resulted in the
discovery of virus
n Infectious
n Filterable agent
n Submicroscopic, non-free living organism (dependent on
live cells)
n Universal existence: Humans, animals (insects), plants
(algae), fungi (mycovirus), bacteria (bacteriophage), amoeba
(megavirus) all can be infected by viruses
§ DNA or RNA as genome, proteins as viral replication
enzymes and protective coat, in some cases with lipids and
carbohydrates (for enveloped viruses), no organelles, no
machinery for protein synthesis and no metabolic activity
n Don’t grow or divide, assembly of individual
components (DNA or RNA and proteins)
Poliovirus (naked, unenveloped) Rhabdoviridae (rabies virus, enveloped)
Capsid, RNA genome
Mammalian cell
[Link]
[Link]
Assembly Locations
Virus structure
n Virion: infectious, complete virus particle: RNA or DNA,
proteins, enveloped viruses have carbohydrates and lipids
n Capsid: composed of repeating protein subunits (protomers)
--- protect viral genome from extracellular nucleases
--- impart structural symmetry to virion (icosahedral or
helical)
--- essential for the infectivity of virion
--- in naked (non-enveloped) virus, the capsid serves as the
attachment protein that bind to host cell receptor
--- most viruses have one capsid, an exception is Reoviridae
that has two capsid layers
--- antigenic and provoke host immune response
n Nucleocapsid: composed of capsid and nucleic acid
§ Envelope: viral membrane, lipid bilayer carrying viral glycoproteins
§ Matrix protein: welds the capsid or nucleocapsid to the envelope.
Enveloped virus
• Envelopes are acquired as nucleocapsids bud through cellular
membranes. These portions of cellular membranes are
modified by virus and contains the viral glycoproteins,
not cellular proteins, and these viral glycoproteins appear
as spikes on the surface of the virus particle
• Functions of spikes (glycoproteins)
-- binding sites for cell surface receptors
-- major antigenic determinants
-- mediates virus fusion with cellular membranes
• Envelopes lack rigidity and therefore usually appear
heterogeneous in shape and size on electron microscope.
• Generally, enveloped viruses are spherical, but exceptions
are bullet-shaped rhabdovirus, brick-shaped pox virus.
Types of capsid
• Icosahedral (isometric) capsid
--- a solid shape containing 12 vertices, 20 triagular
faces and 30 edges arranged around the surface
of a sphere (soccer ball)
--- example: adenovirus
Knob (protomer)
Capsomer (3 protomers)
fiber
Most DNA and (+) RNA viruses have icosahedral capsids.
Types of capsid (cont’)
Adenovirus:
The minimal subunits (one or 30 edges where two faces meet
more proteins) for an
icosahedral capsid structure
is 60 subunits (T=1).
Triagulation number (T): 1, 3 20 triagular
4,7,9,12, 13, 16 and so forth. 12 vertices faces
T=H2+HK+K2 (H.K integers)
Pseudo-triagulation number (P)
: not true icosahedral
Symmetry, but the same
principle
The rules of rotational symmetry are referred to as 2-3-5
symmetry
A simple icosahedral virus
Subunits building block (protomer)
60 subunits (T=1)
β Sandwich (eightfold β barrel)
[Link]
Icosahedral shaped viruses
T=16 T=25
P=7
P=3 T=1
T=13
Cryoelectron microscopy
Larger particles accommodate larger genomes.
Types of capsid (cont’)
• Helical capsid [Link]
--- capsid is made up of a spiral or helix of protein
subunits (protomers)
--- example: Tobacco mosaic virus (TMV, naked or
non-enveloped)
Protomer
2130 protomers (16.3)
Most (-) RNA viruses with envelopes have helical capsids.
Different sizes of genomes can be easily accommodated.
Influenza Virus
Neuraminidase (tetramer)
[Link]
Hemagglutinin (trimer)
Credit: [Link] and Ian Wilson
Why virus needs to be
assembled?
• Protection barrier: nucleic acids (DNA or RNA) are very
sensitive to the nucleases or mechanical shearing and
chemical modifications such as by ultraviolet light (UV)
from the sun light.
• Essential for viral infectivity: in order for viruses to reproduce
themselves in the cells, they need proteins on the surface of
virus to bind to the cell receptors to initiate infection, in
some cases, deliver the genome into the cells
And how to assemble?
• Several RNA viruses undergo self-assembly as a helical
nucleocapsid
--- TMV: Heinz Fraenkel-Conrat and R.C. Williams in 1957
• The symmetry structure is held together by protein- protein,
protein- nucleic acid, and protein-lipid interactions
(hydrophobic and electrostatic)
• Because of symmetry, the structure is in free-energy state and
stable and therefore the favored structure of the components
• Virus start to assemble spontaneously when there are accumulated
viral components
Assembly of poliovirus
HIV-1 Assembly
Front. Microbiol., 20 March 2015 | [Link]
Herpesvirus Assembly
Assembly of bacteriophage T4
Assembly factory
Reovirus infected cell Ebola virus infected cell Herpesvirus infected cells
Virus-like particles (VLPs)
PRRSV VLPs Influenza virus VLPs
PLoS ONE 3(1): e1501. doi:10.1371/[Link].0001501
Virus-like particles:
No genetic materials
Not infectious
Packaging sequence in Herpesvirus
pac ori
Amplicon
Amplicon Vector System
Plasmid
Cotransfection with HSV-1 bacmid lacking
packaging sequences ("helper genome")
Plasmid is replicated into concatemers, cut into
genome-unit length molecules & packaged into
viral particles by the helper genome; the helper Helper-free
itself cannot be packaged amplicons
Taxonomy of virus
Taxonomy of virus
Taxonomic level Suffix (comment) Example
Order -virales Mononegavirales
(a group of related families)
Family -viridae Paramyxoviridae
Subfamily -virinae Paramyxovirinae
Genus -virus Morbillivirus
Species (an individual virus) Measles virus
Classification of viruses
• Classical virus classification scheme
--- type of nucleic acid (DNA or RNA)
--- capsid symmetry (icosahedral or helical)
--- presence or absence of envelope
--- size of virus particles
• Recent classification scheme (ICVT)
--- Genomes
• Baltimore classification
--- based on the pathways viruses used to make mRNA
and to replicate
Origin of family names
Animal Viruses ------
Bunya: Bunyawera, a town in Uganda, Africa Toga: Coat
Reo: Respiratory orphan enteric Parvo: Small
Corona: Halo Irido: Iridescent
Retro: Reverse transcriptase
Adeno: Gland (adenoids) Filo: Filamentous
Rhabdo: Rod (bullet) – shaped Arena: Sandy
Birna: Bi (two RNA segments) Pico: Small
Paramyxo: Related to mucus Orthomyxo: True mucus
Hepadna: Hepatitis/ DNA Pox: Pocks
Papova: Papilloma virus, polyoma virus vacuolating virus
Insect viruses -------
Noda: nodamura: a place in Japan where first isolated.
Baculo: bacillus (rod)-shaped
Virus genome
• DNA viruses:
--- Almost all DNA viruses infecting animals have dsDNA
--- Exceptions are Parvoviridae (parvoviruses and
adeno-associated virus) and Circoviridae (TT virus
related hepatitis) which have ssDNA
• RNA viruses:
--- Almost all RNA viruses have ss RNA
--- Exceptions are Reoviridae (Reovirus, ds RNA)
--- Positive strand (+): same polarity as mRNA (Picornaviridae)
--- Negative strand (-): opposite polarity as mRNA
• all have helical capsid
• some have segmented genome (Orthomyxoviridae)
--- Ambisense RNA genome: both (+) and (-) single strand RNA
(Bunyaviridae and Arenaviridae)
