Lecture 2
Genome Classification and
Structure
The size of viruses
How are viruses classified?
• For the first 60 years there was no system
• Named according to the:
– associated diseases e,g poliovirus, rabies,
– type of disease caused e.g murine leukemia virus,
– sites in the body affected or from which the virus was first
isolated e.g rhinovirus, adenovirus.
– where they were first isolated Sendai virus, Coxsackievirus,
– after scientists who discovered them e.g Epstein-Barr virus,
– or for the way people imagined they were contracted e.g
dengue = ‘evil spirit’; influenza = ‘influence’ of bad air.
• Two systems:
– The Hierarchical
– Baltimore Classification System
The Hierarchical virus
classification system
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In 1962 Lwoff, R. W. Horne, and P. Tournier advanced a
comprehensive scheme for the classification of all viruses consisting of
traditional hierarchical phylum - class - order - family - subfamily - genus species - strain/type.
The most imortant principle embodied in this system was that viruses should be
grouped according to their shared properties rather than the protperties of the
cells or organisms they infect.
Four main characteristics are used:
– Nature of the nucleic acid: RNA or DNA
– Symmetry of the capsid
– Presence or absence of an envelope
– Dimensions of the virion and capsid
At the moment classification is really only important from the level of families
down. Members within a virus family are ordered with Genomics, the elucidation
of evolutionary relationships ba analyses of nucleic acid and protein sequence
similarities.
Structural Classes
•Icosahedral symmetry
•Helical symmetry
•Non enveloped (“naked”)
•Enveloped
Icosahedral capsids
a) Crystallographic structure of
a simple icosahedral virus.
b) The axes of symmetry
Helical Symmetry
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The simplest way to arrange multiple, identical protein subunits is to use
rotational symmetry & to arrange the irregularly shaped proteins around the
circumference of a circle to form a disc.
Multiple discs can then be stacked on top of one another to form a cylinder,
with the virus genome coated by the protein shell or contained in the hollow
centre of the cylinder.
Tobacco mosaic virus (TMV) is representative of one of the two major
structural classes seen in viruses of all types, those with helical symmetry.
Helical symmetry
Closer examination of the
TMV particle by X-ray
crystallography reveals that
the structure of the capsid
actually consists of a helix
rather than a pile of stacked
disks. A helix can be defined
mathematically by two
parameters:
1.The amplitude (diameter)
2. The pitch (the distance
covered by each complete
turn of the helix
TMV, a filamentous virus
Enveloped helical virus
Enveloped icosahedral virus
Enveloped Structure of HIV
Transmission Electron
Micrograph of HIV-1
The nucleocapsid (arrows) can
be seen within the envelope.
The Baltimore Classification
System
• Although many viruses are classified into individual
families based on a variety of physical and biological
criteria, they may also be placed in groups according
to the type of genome in the virion.
• Over 30 years ago virologist David Baltimore devised
an alternative classification scheme that takes into
account the nature of the viral nucleic acid.
Cont..
• One of the most significant advances in virology of the past 30
years has been the understanding of how viral genomes are
expressed.
• Cellular genes are encoded in dsDNA, from which mRNAs are
produced to direct the synthesis of protein.
• Francis Crick conceptualized this flow of information as the
central dogma of molecular biology:
The Baltimore classification system
Based on genetic contents and replication strategies of
viruses. According to the Baltimore classification, viruses
are divided into the following seven classes:
1. dsDNA viruses
2. ssDNA viruses
3. dsRNA viruses
4. (+) sense ssRNA viruses (codes
directly for protein)
5. (-) sense ssRNA viruses
6. RNA reverse transcribing viruses
7. DNA reverse transcribing viruses
where "ds" represents "double strand"
and "ss" denotes "single strand".
Virus Classification I
- the Baltimore classification
• All viruses must produce mRNA, or (+) sense RNA
• A complementary strand of nucleic acid is (–) sense
• The Baltimore classification has + RNA as its central
point
• Its principles are fundamental to an understanding of
virus classification and genome replication, but it is
rarely used as a classification system in its own right
Concept
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By convention, mRNA is defined as a positive (+) strand because it is
the template for protein synthesis.
A strand of DNA of the equivalent sequence is also called the (+)
strand.
RNA and DNA strands that are complementary to the (+) strand are, of
course, called negative (-) strands.
When originally conceived, the Baltimore scheme encompassed six
classes of viral genome, as shown in the figure. Subsequently the
gapped DNA genome of hepadnaviruses (e.g. hepatitis B virus) was
discovered. The genomes of these viruses comprise the seventh
class. During replication, the gapped DNA genome is filled in to
produce perfect duplexes, because host RNA polymerase can only
produce mRNA from a fully double-stranded template
From Principles of Virology Flint et al ASM Press
The seven
“Baltimore”
replication
classes
Virus classification
• This is a based on three principles –
– that we are classifying the virus itself, not
the host
– the nucleic acid genome
– the shared physical properties of the infectious
agent (e.g capsid symmetry, dimensions, lipid
envelope)
How many?
• In 2010 the International Committee on
Taxonomy of Viruses (ICTV) formally
recognized:
– 6 Orders
– 87 Families
– 19 Subfamilies
– 348 Genera
– and 2285 Species of viruses
Naming Viruses
• Order has the suffix – virales e.g
Picornavirales
• All Families have the suffix -viridae e.g.
Caliciviridae, Picornaviridae,
Reoviridae.
• Genera have the suffix -virus.
• E.g Family Picornaviridae there are 5
genera: enterovirus, cardiovirus,
rhinovirus, apthovirus and hepatovirus.
Orders of Viruses
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Caudovirales (3 Families)
Herpesvirales (3 Families)
Mononegavirales (4 Families)
Nidovirales (3 Families)
Picornavirales (5 Families)
Tymovirales (4 Families)
Virus families not assigned to an
order (65 Families)
Picornavirales
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Viruses with vertebrate, insects and plant hosts.
This group consists of viruses which have (+) sense single stranded RNA
genomes.
Share a number of common features:
– conserved RNA-dependent RNA polymerase
– genome has a protein attached to the 5' end
– no overlapping open reading frames within the genome
– all the RNAs are translated into a polyprotein before processing
Families within this group:
– Dicistroviridae (2 Genera)
– Iflaviridae (1 Genus)
– Marnaviridae (1 Genus)
– Picornaviridae (12 Genera)
– Secoviridae (1 Subfamily and 5 Genera not in a Subfamily)
Picornaviridae
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Aphthovirus (3 Species)
Avihepatovirus (1 Species)
Cardiovirus (2 Species)
Enterovirus (10 Species)
Erbovirus (1 Species)
Hepatovirus (1 Species)
Kobuvirus (2 Species)
Parechovirus (2 Species)
Sapelovirus (3 Species)
Senecavirus (1 Species)
Teschovirus (1 Species)
Tremovirus (1 Species)
Enteroviruses
• Cause a wide range of infections.
• Poliovirus, the prototypical enterovirus, can cause a
subclinical or mild illness, aseptic meningitis, or
paralytic poliomyelitis, a disease that has been
eradicated in most parts of the world.
• The nonpolio viruses (group A and B
coxsackieviruses, echoviruses, enteroviruses)
continue to be responsible for a wide spectrum of
diseases in persons of all ages, although infection
and illness occur most commonly in infants.
RNA viruses
From Principles of Virology Flint et al ASM Press
DNA viruses
From Principles of
Virology Flint et al
ASM Press
Coronavirus
(+) RNA genome encodes
five translational reading
frames.
The capped and poly-A
subgenomic mRNAs have
the same 5’ leader and
nested 3’ sequences.
NO splicing “skipping” RNA Pol
Influenza A
Multipartite genome of eight
helical nucleocapsid
segments of (-) strand RNA