MIC 303; C; 2.0
ANJORIN, A. A.,
Virology & Immunology Research Group,
Department of Microbiology,
Lagos State University, Ojo
Introduction and Objectives
Principles of Viral Taxonomy
Criteria for Viral Classification
Family of Subviral Agent
Our elementary understanding
At the end of our discussion, we should all be able to:
INTRODUCTION AND OBJECTIVES
DEFINITIONS IN VIRAL TAXONOMY
The word Viral is from Virus
Obligate intracellular entity
The word taxonomy –A Science with dynamic field, based on
Uses techniques and theories of:
-Collating and describing; identification and classification;
grouping and naming of viruses
But Nomenclature is just naming
Acronym ICNV ICTV
Virology, > 100yrs; Viral taxon (ICNV, 1960; ICTV, 1966 )
Systematics is the science of organizing the history of the evolutionary
relationships of organisms.
Classification is determining the evolutionary relationships between organisms.
Identification is recognizing the place of an organism in an existing
classification scheme, often using dichotomous keys to identify the organism.
Taxonomy (nomenclature) is assigning scientific names according to agreed
international scientific rules.
The official taxonomic groups (from the largest to the smallest are):
Kingdom (e.g., animals, plants, bacteria; does not apply to viruses)
Phylum (e.g., vertebrates; does not apply to viruses)
Class (group of related orders; does not apply to viruses)
Order (group of related families)
Family (group of related genera)
Genus (group of related species)
Species, the smallest taxonomic group
Formed and governed by the Virology Division of the
International Union of Microbiological Societies (IUMS)
ICTV is composed of member Executive Committee
(world experts on viruses) supported by numerous
subcommittees and study groups
Operates an authoritative database (ICTVdB)
containing taxonomic information
Presents report to International Congress of Virology
Update publication on taxonomy at approximately 3-
ICTV official objectives are to:
develop an internationally agreed taxonomy for viruses
develop internationally agreed names for taxa,
including species and subviral agents
communicate decisions to all users particularly the
international community of virologists
maintain an index of virus names
maintain an ICTV database, that records the data that
characterize each named viral taxon, with their common
names in all major languages
ICTV 2011Official taxonomy
ICTV Classification system is Non systematic based upon the
opinionated usage of data
Estimated 400,000 different viruses virologist believe may exist
Today > 5,000 viruses have been identified.
Number of recognized hierarchical taxa include:
94 families ( > 24 families cause disease in human)
22 Sub families
The Order taxonomy
Classification of the 6 orders include:
Order: Caudovirales(3 Families)
Order: Herpesvirales(3 Families)
Order: Mononegavirales(4 Families)
Order: Nidovirales(3 Families)
Order: Picornavirales(5 Families)
Order: Tymovirales(4 Families)
72 Virus families are yet to be assigned to order
Viral Taxonomy Methods
A monothetic system of classification is defined as a
system based on a single characteristic or a series
of single characteristics.
Polythetic is defined as sharing a number of
common characteristics, without any one of these
characters being essential for membership
System that is currently being used is a
-Non systematic, polythetic, hierarchical system.
-Differs from any other system in use for other
organisms but it is effective, useful, and has withstood
the test of time
Using the polythetic approach, a given virus grouping is
defined by a collection of properties rather than a
-and virus groups in different branches of the taxonomy
can be characterized by different collections of
BASIC TERMS IN VIRAL TAXONOMY
Entire infectious viral particle in nature
- They are the smallest known plant pathogens
- They consist of a circular, single-stranded RNA that does not encode a protein
(Cho et al., 2013)
- the smallest known infectious agents.
They are much smaller than the smallest genomes of viruses and have no genes
for encoding proteins.
After invading a host cell, viroids are thought to mimic the cell's DNA, so that
the cell's RNA polymerase replicates them in the nucleus. Viroids are believed
to cause disease by interfering with the host cell's gene regulation. They are
destructive to many important commercial plants, including potatoes, tomatoes,
cucumbers, coconuts, and chrysanthemums.
-SSRNA satellite viruses; larger RNA to viroid
-Consist of a single-stranded RNA genome encapsidated in stolen
capsid of helper virus i.e. No gene to code for their own structural
the smallest of viruses; a plant virus with its RNA arranged in a
circular chromosome without a protein coat.
A virusoid is an infectious agent that infects plants in conjunction with
an assistant virus; the assistant virus harbours the virusoid and is
required for successful infection.
Virusoids, while being studied in virology, are not considered as
viruses but as subviral particles. Since they depend on helper viruses,
they are classified as satellites.
-Proteinacious infectious particle i.e. Possess Capsid +
NA together in Association
-N.A. (About 10-12nm)
-Also Non Immunogenic
-A.k.a factory site/ site for assembly of sub viral particles
-Modified region where active viral replication takes
place in a viral infected cell
-A defective virus
-Depends on helper virus for its replication.
- A virus which is unable to replicate because it lacks a
VIRAL TAXONOMICAL RULES
Nomenclature and Classification of viruses do
not Use Conventional Taxonomic Groups
The nucleic acid of DNA viruses is usually double
stranded(ds) linear or circular molecules with the exception
of parvovirus which has single stranded(ss) DNA.
The nucleic acid of RNA viruses is usually single stranded(ss)
with the exception of the reoviruses (dsRNA)
In Sense (positive/plus strand viruses), the genome has the
same polarity as the viral mRNA and thus can function as
In Antisense (negative/minus strand viruses), the genome has
the polarity opposite to that of the mRNA and therefore
cannot be translated into proteins until it has first been
transcribed into a complementary strand
Rules for Taxa
A species name shall consist of as few words as practicable
but must not consist only of a host name and the word virus.
A species name must provide an appropriately unambiguous
identification of the species.
Numbers, letters, or combinations thereof may be used as
species where such numbers and letters are already widely
Newly designated serial numbers, letters or combinations
thereof are not acceptable alone as species epithets. If a
number or letter series is in existence it may be continued.
A virus genus is a group of related species that
share some significant properties and often only
differ in host range and virulence.
A genus name must be a single word ending in virus.
Approval of a new genus must be accompanied by
the approval of a type species.
A subfamily is a group of genera sharing certain
Taxon shall be used only when it is needed to solve
a complex hierarchical problem.
A subfamily name must be a single word ending
A family is a group of genera, whether or not these
are organized into subfamilies, sharing certain
A family name must be a single word ending
An order is a group of families sharing certain
An order name must be a single word ending
CRITERIA FOR VIRAL CLASSIFICATION
N. A. type
2. RNA viruses
Nature and Strandedness
Nature can be:
Segmented/ Non segmented genome or
Based on Polarity.
I. Sense strand (positive/plus strand)
II. Antisense strand
I. Sense strand (Positive/plus strand)
The genome has the same polarity as the viral
mRNA and thus can function as mRNA
A ssRNA+ means a genome with full, correct
information, in the right position and can act
as a template for translation
II. Antisense strand (Negative/minus strand)
The genome has the polarity opposite to that
of the mRNA and therefore cannot be
translated into proteins until it has first been
transcribed into a complementary strand
Strandedness can be Single-stranded (ss) or double-stranded (ds)
ss RNA + ve
ds RNA-/ + ( - means Abnormal/ + because it is double stranded)
ss DNA – ( - means Abnormal because DNA should be doubled)
ds DNA +/ -
There is another ss RNA + ve for Retro viruses called (ss Retro
And there is also ss RNA that is negative known as (ss RNA –ve)
Classification of Viruses based on Genomic composition
and their Pathway of mRNA formation
Haemagglutinin enzyme (H) contained in the spike and is
required for adsorption and penetration of Orthomyxo viruses
into the host cells.
Neuraminidase enzyme (N) contained in another type of spike
and it is required for invasion and release of influenza viruses
-RNA-dependent RNA polymerase in RNA viruses
-DNA polymerase in smallpox virus
-RNA-dependent DNA polymerase (Reverse transcriptase) in
hepatitis B viruses and retroviruses
Others DNA Viruses
Ds non enveloped
Ss non enveloped
B. RNA VIRUSES
(Latin: Arenosus- Sandy)
A. Subgroup Tacaribe Complex
(New world arenaviruses)
Lymphocytic Choriomeningitis V.
B. Subgroup LCM-LASV Complex
(Old world arenaviruses)
Lassa Fever Virus
(Greek Astron- Star-like)
(Sigla, Bi-Double Stranded genome).
Three Genera affecting fish, chickens and insects:
Borna Disease Virus
Seven groups (19 viruses) and
22 ungrouped viruses:
Genus Bunyavirus e.g.
Bunyamwera, La Cross virus
Genus Hantavirus e.g. Hantaan
Genus Phlebovirus e.g. Rift VFV
Genus Nairovirus e.g. Crimean-
Congo Haemorrhagic Fever Virus
Flaviviridae (Greek Flavus- Yellow)
1. Pestivirus (Bovine Diarrhoae virus)
2. Hepatitis C-like viruses (Hepatitis
C and G Viruses)
3. Genus Flavivirus
Yellow Fever V. (Aedes aegypti).
2 types: Urban &Jungle
West Nile Virus (Uganda West Nile
Potiskum Virus (Mice, 1969)
Zika Virus (Uganda Zika forest
Monkey, 1947, Also Nigeria)
(Greek Ortho-Straight, Myxo- Mucous)
Surface projections of envelope
distinct; About 500 spikes
8 gene segments (PB1, PB2, PA, HA, NP, NA, M, NS).
-Epidemics and pandemics by
Antigenic Drift (accumulation of point
mutations=Gradual changes) and
Shift (major antigenic changes=new
subtype into human population).
1. Genus Influenzavirus A
2. Genus Influenzavirus B
3. Genus Influenzavirus C
4. Genus Thogoto-like Viruses
Paramyxoviridae (Greek Para- By the side of; Myxo-)
e.g. Human paramyxovirus
and H parainfluenza 1
Genus Morbilivirus e.g.
Genus Rubulavirus e.g.
(Sigla, Greek Pico- Small)
1. Genus Enterovirus e.g.
Enteroviruses 68, 70, 71
Polio Virus and Coxsackie
2. Genus Rhinovirus
Human rhinovirus 1A
3. Genus Hepatovirus
Human hepatitis A virus
4. Genus Cardiovirus
5. Genus Aphthovirus
Foot and Mouth Disease V.
Reoviridae (Sigla, R.E.O. ).
Four Genera- Medicals.
Genus Orthoreovirus- Human
Genus Rotavirus- Human rota
Genus Coltivirus- Colorado
Tick fever Virus
Genus Orbivirus-Orungo V.
Cypovirus e.g. Cypovirus type
There are five species of : A, B, C, D, and E
3 Human rotaviruses: A, B and C
Rotavirus A: Different strains called serotypes
6 structural (viral) proteins: VP1, VP2, VP3, VP4, VP6
6 NSPs only produced in cells infected by rotavirus:
NSP1, NSP2, NSP3, NSP4, NSP5 and NSP6
2 genes determine G-types and P-types of A
Glycoprotein VP7 defines the G serotypes (G1-
6,891012) and protease- sensitive protein VP4 defines
P serotypes (P1, 4, 6, 8-11)
Retroviridae (Sigla, Reverse transcriptase)
1. Genus Gammaretroviruses
2. Genus Episilonretroviruses
3. Genus Alpharetroviruses
4. Genus Betaretrovirus group
5. Genus Deltaretroviruses
6. Genus Lentivirus e.g.
Human T- Leukaemia Virus
Type 1 and 2
7. Genus Spumavirus
Genus Vesiculovirus e.g.
Genus Lyssavirus e.g.
(Latin Toga- Mantle or Cloak, A
Cover/ layer) because the virions are
surrounded by a lipid envelope and
1. Genus Alphavirus
Igbo-Ora Virus; Sindbis virus
2. Genus Rubivirus
Rubella (from latin word- little red)
Virus (German measles)
Only virus of the Genus
(Latin Torus- Lowest Convex)
Some consider Torovirus as a Genus in the family
Others RNA Viruses
TAXONOMY OF SUBVIRAL AGENTS
-Taxonomical Properties of subviral agents include:
i. No Genome
ii. No I.R.
iii. Filterable size
iv. No inactivation by heat, disinfectant and UV light
v. Tend to be modified human protein that is infectious
vi. Usually tend to form insoluble aggregate of fibrils
vii. Only Clinical diag. but just one Lab. Diag.:
Histology of Brain
Rules in Naming sub-viral agents
Classical example; Endings for taxa of viroids are:
Word viroid for species
Suffix -viroid for genera
-viroinae for sub-families and
-viroidae for families
Classification of Subviral agents
1. FAMILY DELTAVIRIDAE
2. SLOW VIRUSES
1. FAMILY DELTAVIRIDAE
-One Genus: Deltavirus
-Contains Hepatitis D virus a.k.a Delta agent
-A defective RNA virus, replicates in HBV infected
2. SLOW VIRUSES
-Prions, Proteinacious infectious or prion protein (Prp) agent
referred to as unconventional viruses
-Cause group of Diseases called Prion Diseases known as
Transmissible Spongiform Encephalopathy (TSE)
a. Human (Kuru, Cannibalism; 1957; 1st among fore tribe in
eastern island of Papua New Guinea)
Creutzfeldt- Jakob Disease;
Gerstmann- Straussler Scheinker (GSS) Disease;
Fatal familial insomnia(FFI)
b. Animal (Scrapie, Mad Cow Dis, Bovine Spongiform
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