2. Acknowledgement
First we are very thankful to ‘Delhi University’
who gave us the path to express our creativity by
these presentations. I also thankful to Dr.
Srivastava and to the classmates to see this. This
ppt will introduce you about different virus
Classification and Nomenclature of viruses
3. Index
• Classification
• Defination
• Reseon beyond classification
• Criteria of virus classification
• Differant way of clasification
• Holmes classification
• LHT classification
• Casjens and Kings classification of virus
• ICTV classification
• Nomenclature
• Conclusion
• Question
4. • The arrangement of organisms OR
Viruses into groups based on
mutual similarity or evolutionary
relatedness.
5. 1. Disease symptoms
Useful in clinical situations
• Host organism
implies a fixed link between virus and
host-Small pox, HBV
• Physical structure of the virus particle
Envelope vs no envelope
Helical or isocahedral
Alls these approaches fail to predict fundamental features of the viruses
Classical criteria for classification
6.
7. Modern Criteria for classification
Based on genome composition and structure
allows you to:
1) deduce the basic steps that must take place to produce mRNA
2) simplifies comprehension of the life cycle of virus
Baltimore classification
8. Holmes Classification
• Holmes (1948) used carolus linnaeus`s
binomial namenclature system to classify
virus
• He classify virus into three group under
one order,virales
11. • Lwoff :-born in Ainay-le-Château, Allier, in Auvergne, France,
• son of Marie (Siminovitch), an artist, and Solomon Lwoff, a
psychiatrist.Joined the Institute Pasteur in Paris when he was 19 years
old.Awarded a Nobel Prize in Medicine in 1965 for the discovery of the
mechanism that some viruses (which he named proviruses) use to infect
bacteria.
• Paul Tournier:- (May 12, 1898 – October 7, 1986) was a Swiss
physician and author
• Worne:-The electron microscope reveals that these infectious particles
possess three principal types of symmetry. Each species of virus is
ingeniously assembled from just a few kinds of building block
12. 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
• number of the capsomers
The Provisional Committee on Nomenclature of
Virus (PNVC),the International Association of
microbiological Societies (1962)
14. Subphylum Deoxyvira
(DNA viruses)
Class Deoxyhelica
(Helical symmetry)
Class Deoxycubica
(cubical symmetry)
Class Deoxybinala
(dual symmetry)
Order Urovirales
Family Phagoviridae
Order Chitovirales
Family Poxviridae
Order Peplovirales
Family Herpesviridae
(162 capsomeres)
Order Haplovirales
(no envelope)
Family Iridoviridae (812 capsomeres)
Family Adenoviridae (252 capsomeres)
Family Papiloviridae (72 capsomeres)
Family Paroviridae (32 capsomeres)
Family Microviridae (12 capsomeres)
15. Subphylum Ribovira
(RNA viruses)
Class Ribocubica Class Ribohelica
Order Togovirales Order Lymovirales
Family Arboviridae Family Napoviridae
Family Reoviridae
Order Sagovirales Order Rhabdovirales
Family Stomataviridae
Family ramyxoviridae
Family Myxoviridae
Suborder Flexiviridales Suborder Rigidovirales
Family Mesoviridae
Family Peptoviridae
Family Pachyviridae
Family Protoviridae
Family Polichoviridae
16. Casjens and Kings classification of virus
I. Casjens and Kings(1975) classified virus into 4
groups based on
1.type of nucleic acid ,
2.presence of envelope, 3.symmetry
and site of assembly.
17. Casjens and Kings classification
of virus
• Single Stranded RNA Viruses
• Double Stranded RNA Viruses
• Single Stranded DNA Viruses
• Double Stranded DNA Viruses
It is as follows
18. International Committee on Taxonomy of Viruses
(ICTV) classification
• Established in 1966
• Only body to takes the task of developing
refining and maintaining the universal virus
taxonomy
• governed by the Virology Division of the
International Union of Microbiological
Societies.
19. ICTV classification
Viral classification starts at the level of order and
continues as follows, with the taxon suffixes
Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species
Species names generally take the form of
[Disease] virus.
20.
21.
22.
23.
24. Caudovirales
• Known as the tailed bacteriophages.
• Have double stranded DNA (dsDNA) genomes
• Have a distinct shape; each virion has an icosohedral head
that contains the viral genome, and is attached to a flexible tail
by a connector protein
• At least 350 recognised species in this order.
• Contain the three families
• The three families are defined on the basis of morphology.
• All viruses differ in the length and contractile abilities of their
tails
• Classification scheme was originated by Bradley in 1969
26. Family: Myoviridae
• a family of bacteriophages
nonenveloped
consist of a head and a tail separated by a neck
head has a diameter of 50–110 nm
icosahedral symmetry
it is composed of 152 capsomers that are hexagonal
in outline.
tubular tail has helical symmetry and is 16-20
nm in diameter
It consists of a central tube, a contractile
sheath, a collar, a base plate, six tail pins and
six long fibers. It is similar to Tectiviridae
27. Family: Myoviridae
• Morphology
Nonenveloped
Consist of a head and a tail separated by a neck.
head has a diameter of
50–110 nm and has
icosahedral symmetry
it is composed of
152 capsomers that
are hexagonal in
outline
tubular tail has helical symmetry
and is 16-20 nm in diameter
consists of a central tube, a
contractile sheath, a collar,
a base plate, six tail pins
and six long fibers
a myovirus' tail is permanent
Contractions of the tail require ATP. On contraction of the sheath, sheath subunits
slide over each other and the tail shortens to 10–15 nm in length
Have long tails that are contractile
28. Genome
• Linear, Double-stranded DNA . It has terminally
redundant sequences. The GC-content is ~35%. The
genome encodes 200-300 proteins that are
transcribed in operons.5-Hydroxymethylcytosine may
be present in the genome (instead of thymidine)
Life cycle
Myoviruses are in general lytic, lacking the genes required to
become lysogenic
(t=spounap2o3.12)at least 130 species in this family.
30. Subfamily: Peduovirinae
• Heads of 60 nm in diameter and Tails of 135
nm.contracted sheaths tend to slide off the tail core
• P" phage is the type species
• Genus P2likevirus; type species:
Enterobacteria phage P2
• Genus Hpunalikevirus: Type Species:
Haemophilus phage HP1
31. Subfamily: Peduovirinae
• heads of 60 nm in diameter and
• tails of 135 nm
contracted sheaths tend to slide off the tail core
P" phage is the type species
Genus P2likevirus; type species: Enterobacteria phage P2
Genus Hpunalikevirus: Species: Haemophilus phage
HP1
34. Subfamily Spounavirinae
• broad-host range phages that infect
members of the Firmicutes.
Isometric heads of 87-94 nm in diameter
Striated 140-219 nm long tails and a double base plate
This subfamily is derived from SPO plus una (Latin for one).
Genus Spounalikevirus: type species: Bacillus phage SPO1
Genus: Twortlikevirus
Genus: Unassigned
Species: Staphylococcus phage Twort
37. Subfamily: Tevenvirinae
• type species Enterobacteria phage T4
• moderately elongated heads of about 110 nanometers
(nm) in length
• 14 nm long tails with a collar, base plates with short
spikes and six long kinked tail fibers
• genera within this subfamily are divided on the basis of
head morphology
• genus T4likevirus having a head length of 137 nm
• genus Schizot4likevirus being 111 nm in length
• Within the genera on the basis of protein homology the
species have been divided into a number of groups
39. Family: Podoviridae
• characterized by having very short,
noncontractile tails
morphology
nonenveloped
a head-tail structure .9 structural proteins
head is ~60 nanometers (nm) in diameter,
consists of 72 capsomers
icosahedral with a T = 7 symmetry.
The head protein has a molecular mass of ~38
kiloDaltons
and is present in 460 copies per virion.
The tail is non-contractile
has 6 short subterminal fibers.
It is thick and rod-shaped
built of stacked disks.
The maximum length is ~17 nm.
40. Family: Podoviridae
• viruses tend to be lytic rather than
lysogenic.
double stranded DNA
genome is linear ~40–42 kilobases in length
encodes ~55 genes.
The guanine + cytosine content is ~50%.
It has terminally redundant sequences and
is nonpermuted. By weight, the genome
constitutes ~50% of the viron.
Genome
This classification is based on the timing of transcription that is temporally
regulated.
Genes with related functions are clustered together.
Genome replication is bidirectional.
(autographipicO2.6.8UNSIN)
bpp1n4p22luz24#15pco32
42. Subfamily: Autographivirinae
Refers to the “auto-graphein” or “self-
transcribing”
phages which encode their own (single
subunit) RNA polymerase, a common
characteristic among its members.
Contain 3 genera and 1 unassinged genus
phimvsp6t7
44. Subfamily: Picovirinae
• pico=very small,virinae=suffix for subfamily
• have a relatively small dsDNA genome (between 16-20 kbp) (hence
the term pico-virinae)
• a typical protein primed DNA polymerase for replication, a property
shared with the Tectiviridae family.
• contains two genera
• Phi29likevirus
• Ahjdlikevirus, to infect and lyse Clostridium perfringens
• unassigned species
• Actinomyces phage Av-1 and
• Streptococcus phage Cp-1.
• This subdivision is based on genome organization and
resemblance at the proteome level.
•
• phi29AaHJaD
Synonyms Nanovirinae
45. • Proposed Genera
Genus P60likevirus (synonyms = Marine Picocyanobacteria Podovirus
subgroup or MPP subgroup);
type species: Synechococcus phage P60
• Genus Cpv1likevirus;
• type species: Clostridium phage CpV1
Genus 119xlikevirus;
• type species: Pseudomonas phage 119X
Genus Vp2likevirus;
• type species: Vibrio phage VP2
Genus Gap227likevirus;
• type species: Cronobacter phage vB CsaP GAP227
• Yersinia phage phiR8-01
• Yersinia phage phi80-18
• Aeromonas phage phiAS7
• Genus Phiys61likevirus;
• type species: Weissella phage phiYS61
46. Family: Siphoviridae
• nonenveloped head and noncontractile tail
about 60 nanometers in diameter
Have an icosahedral capsid (morphotype B1) or a prolate capsid
(morphotype B2)
double stranded and linear.
It is typically about 50 kilobases in length
contains about 70 genes.
The guanine/cytosine content is usually around 52%
(c2l5n15t5 lemdaspbetaua10G)
genome
capsids have no envelope and are generally about 60 nanometers in diamete
52. Order: Herpesvirales
Viruses having a capsid structure that consists of
a DNA core surrounded by an icosahedral
capsid consisting of 12 pentavalent and 150
hexavalent capsomeres.
double-stranded DNA viruses
genome contains terminal and internal reiterated
sequences
infect animals - both vertebrate and invertebrate.
this order currently has 3 families, 3 subfamilies
plus 1 unassigned, 17 genera, 90 species and
plus 48 as yet unassigned viruses.
54. Family: Alloherpesviridae
• includes the species that infect fish and
amphibians.
created in 2005
Four genera
Genus: Batrachovirus (2 Species)
Species: Ranid herpesvirus
Genus: Cyprinivirus (4 Species)
Cyprinid herpesvirus 3 ...
Genus: Ictalurivirus (3 Species)
Species: Ictalurid herpesvirus 1
Genus: Salmonivirus (3 Species)
Species: Salmonid herpesvirus 1
{batra c ectaluri salman
may be divided into two clades viruses from cyprinid and anguillid hosts
viruses from ictalurid, salmonid,
acipenserid and ranid hosts.
55. Family: Herpesviridae
• large family of DNA viruses that cause
diseases in animals, including humans
known as herpesviruses
herpein ("to creep"), referring to the latent,recurring infections typical of this
group of viruses
More than 90% of adults have been infected
more than 130 herpesviruses, and some are
from mammals, birds, fish, reptiles,
amphibians, and molluscs
establish lifelong infections
56. Genome
• large double-stranded, linear DNA
Encased within an icosahedral protein cage called the capsid
wrapped in a protein layer called the
tegument containing both viral
proteins and viral mRNAs
first isolated from the blue wildebeest in 1960 by veterinary scientist Walter Plowright
64. Subfamily: Betaherpesvirinae
• distinguished by reproducing less quickly than other
subfamilies
• establish latency (site where virus lies dormant until
reactivated) in leukocytes
• four known member species of the Betaherpesvirinae
subfamily that are infectious for humans
• Human cytomegalovirus (HCMV), also known as human
herpesvirus 5 (HHV-5),
• Human herpesvirus 6A and 6B (HHV-6A and HHV-6B),
which were classified as distinct species in 2012,[1]
• Human herpesvirus 7 (HHV-7
• divided into the following four genera
66. Subfamily:
Gammaherpesvirinae
• distinguished by reproducing at a more
variable rate than other subfamilies
• replicate and persist in lymphoid cells but
some are capable of undergoing lytic
replication in epithelial or fibroblast cells
• lytic cycle
• subdivided into the following four genera:
69. Family: Malacoherpesviridae
• a family of DNA viruses that cause
diseases in molluscs.
derived from Greek word 'μαλακός (malacos) meaning 'soft' and
from Greek word 'μαλάκιον (malakion) meaning 'mollusc
may have the ability to infect across species, a feature not
typically observed in vertebrate herpesviruses. This ability
appears to be restricted to related mollusc species
71. Order: Ligamenvirales
• linear viruses that infect archaea of the kingdom
Crenarchaeota
• have double-stranded DNA genomes
• established by D. Prangishvili and M. Krupovic in 2012.
• derived from the Latin ligamen, meaning string or thread.
• virons are filamentous with a helical nucleocapsid
• genome is non segmented linear double stranded DNA.
• two families in this order –
73. Family: Lipothrixviridae
• a family of viruses that infect archaea.
infect thermophilic archaea in the kingdom Crenarchaeota
enveloped and rod-shaped
capsid varies considerably in length - 410-1950 nanometers (nm) - and is 24-38 nm
in diameter
bilayer structure and includes glycolipids and phospholipids
From either end of the viron are protrusions extending from the core through the envelope
capsid itself is elongated and exhibits helical symmetry
with viruses from the Rudiviridae family
linear dsDNA genomes
74.
75. Family: Rudiviridae
• unenveloped
• rod-shaped viruses
genome is composed of linear dsDNA and ranges from 24 kb (ARV1) to 35 kb
(SIRV2
The G+C content only 25%
can act as a template for site-selective and spatially controlled chemical
modification
SIRV1 is about 830 nm and SIRV2 is about 900 nm long
77. Order: Mononegavirales
• derived from the Greek adjective
• μóνος [monos] (alluding to the monopartite
and single-stranded genomes of
mononegaviruses),
• the Latin verb negare (alluding to the
negative polarity of these genomes), and
the taxonomic suffix -virales (denoting a
viral order)
78. Order inclusion criteria
genome is a linear,
nonsegmented,
single-stranded,
non-infectious RNA of negative polarity;
possesses inverse-complementary 3' and 5' termini;
is not covalently linked to a protein
its genome has the characteristic gene order
3'-UTR–core protein genes–envelope protein genes–RNA-dependent RNA polymerase
gene–5'-UTR
it produces 5–10 distinct mRNAs from its genome via polar sequential transcription
from a single promoter located at the 3' end of the genome;
mRNAs are 5' capped and polyadenylated
it replicates by synthesizing complete antigenomes
it forms infectious helical ribonucleocapsids as the templates for the synthesis of
mRNAs, antigenomes, and genomes
it encodes an RNA-dependent RNA polymerase (RdRp) that is highly homologous to
those of other mononegaviruses
it forms enveloped virions with a molecular mass of 300–1,000×106; an S20W of
550–>1,045; and a buoyant density in CsCl of 1.18–1.22 g/cm3
currently includes the five virus families
80. Family: Bornaviridae
• the smallest genome (8.9 kilobases) of any
Mononegavirales species
• to replicate within the host cell nucleus.
• isolated from a diseased horse in the 1970s
• linear negative-sense single stranded RNA virus
• Avian bornavirus is a member of this family. It causes
Proventricular Dilatation Disease in many birds
• History
• The Borna disease was first described in 1885 as
"heated head disease" of cavalry horses in 1885 in the
town of Borna, Germany
82. Filoviridae
• the taxonomic home of several related
viruses that form filamentous infectious
viral particles
• genome in the form of single-stranded
negative-sense RNA
• was created in 1982
• derived from the Latin noun filum (alluding
to the filamentous morphology of
filovirions)
cuava abola margberg
85. Paramyxoviridae
• (from Greek para-, beyond, -myxo-, mucus or
slime, plus virus, from Latin poison, slime)
• are negative-sense single-stranded RNA viruses
responsible for a number of human and animal
diseases.
• enveloped and can be spherical, filamentous or
pleomorphic
• Fusion proteins and attachment proteins appear
as spikes on the virion surface
• nucleocapsid core is composed of the genomic
RNA, nucleocapsid proteins, phosphoproteins
and polymerase proteins.
86. Genome
• non-segmented negative-sense RNA, 15–19 kilobases in
length and contains 6–10 gene
• Extracistronic (non-coding) regions include
• genomes follow the Rule of Six Members of the
sub-family Pneumovirinae do not follow this rule
• Gene sequence within the genome is conserved across
the family due to a phenomenon known as
transcriptional polarity
• The gene sequence is:
• Nucleocapsid – Phosphoprotein – Matrix – Fusion –
Attachment – Large (polymerase)
87. Family: Paramyxoviridae
• Subfamily: Paramyxovirinae (7 Genera)
• Subfamily: Pneumovirinae (2 Genera)
respirorubila and hanipa morbili go to ferlaavula
91. Rhabdoviridae
• derived from the Greek rhabdos meaning rod
• infect a broad range of hosts throughout the animal and
plant kingdoms
• genetic material in the form of negative-sense single-
stranded RNA
• They typically carry genes for five proteins: large protein
(L), glycoprotein (G), nucleoprotein (N), phosphoprotein
(P), and matrix protein (M)
• Rhabdoviruses that infect vertebrates are usually bullet-
shaped.
•
• cytonovinucleopelysa
94. Order: Nidovirales
• the Latin nidus, meaning nest,
• produce a 3' co-terminal nested set of
subgenomic mRNA's during infection
• have positive-sense, single-stranded RNA
genomes
• expresses structural proteins separately
from the nonstructural ones
97. Family: Arteriviridae
• enveloped
• an icosahedral core
• positive-sense RNA genome
• ability to establish prolonged or true
persistent infection in their natural hosts
98. Coronaviridae
• enveloped
• positive-single stranded RNA viruses
• viral genome is 26–32 kb in length
• The 5' and 3' ends of the genome have a cap and poly (A) tract
• genomes contain cis-acting RNA elements that ensure the specific
replication of viral RNA by a virally encoded RNA-dependent RNA
polymerase
• Virions are spherical, 120–160 nm across (Coronavirinae),
bacilliform, 170–200 by 75–88 nm (Bafinivirus) or found as a mixture
of both
• particles are typically decorated with large (~20 nm), club- or petal-
shaped surface projections (the “peplomers” or “spikes”)
• Subfamily: Coronavirinae (4 Genera)
• Subfamily: Torovirinae (2 Genera)
99. Subfamily: Coronavirinae
• phylogenetically compact genogroups of
enveloped,
• positive-sense,
• single-stranded RNA and with a nucleocapsid of
helical symmetry
• genomic size of coronaviruses ranges from
approximately 26 to 32 kilobases
• genus alphacoronavirus and betacoronavirus
derive from the bat gene pool.
• The genus gammacoronavirus includes all avian
coronaviruses identified until 2009
102. Order: Picornavirales
• +) sense single stranded RNA genomes
• 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
103. Order: Picornavirales
• Family: Dicistroviridae (2 Genera)
• Family: Iflaviridae (1 Genus)
• Family: Marnaviridae (1 Genus)
• Family: Picornaviridae (26 Genera)
• Family: Secoviridae (1 Subfamily
and 5 Genera not in a Subfamily)
• Family: Unassigned (2 Genera)
104. Dicistroviridae
• a family of Group IV (positive-sense ssRNA)
insect-infecting viruse
• insects commonly infected by dicistroviruses
include aphids, leafhoppers, flies, bees, ants,
silkworms.
• name (Dicistro) is derived from the characteristic
dicistronic arrangement of the genome
• structural protein genes at the 3' end rather than
the 5' end (as found in Iflavirus, Picornaviridae
and Sequiviridae) and by having 2 genomic
segments rather than a single one (as in the
Comoviridae).
106. Family: Picornaviridae
• means " little RNA virus" (pico means
"very small" in Greek; pico + RNA virus)
• capsid is an arrangement of 60 protomers
in a tightly packed icosahedral structure.
• Each protomer consists of 4 polypeptides
known as VP (viral protein)1, 2, 3 and 4
• icosahedral
• Depending on the type and degree of
dehydration the viral particle is around 27–
30 nm in diameter
107. Genome
• non-segmented and positive-sense (the
same sense as mammalian mRNA, being
read 5' to 3')
• do not have a 5' cap
• have a poly(A) tail at the 3' end
• un-translated region (UTR) at both ends
• RNA genome of between 7.2 and 9.0 kb
(kilobases) in length.
108. History
In 1897, foot-and-mouth disease virus (FMDV), the
first animal virus, was discovered.
FMDV is the prototypic member of the Aphthovirus
genus in the Picornaviridae family
The plaque assay was developed using poliovirus.
Both RNA dependent RNA polymerase and
polyprotein synthesis were discovered by studying
poliovirus infected cells
114. Order: Tymovirales
• have (+) sense single stranded RNA
genomes without DNA intermediates.
• genetic material is protected by a special
coat protein
121. The objectives of the ICTV
• To develop an internationally agreed taxonomy for
viruses
• To develop internationally agreed names for virus taxa,
including species and subviral agents
• To communicate taxonomic decisions to all users of
virus names, in particular the international community of
virologists, by publications and via the Internet
• To maintain an index of virus names
• To maintain an ICTV database on the Internet, that
records the data that characterize each named viral
taxon, together with the common names of each taxon in
all major languages
123. principles of Nomenclature
• The essential principles of virus nomenclature are:-
• (i) to aim for stability;
• (ii) to avoid or reject the use of names which might cause error or confusion;
• (iii) to avoid the unnecessary creation of names.
• Nomenclature of viruses is independent of other biological nomenclature.
Virus taxon nomenclature is recognized as an exception in the proposed
International Code of Bionomenclature (BioCode).
• The primary purpose of naming a taxon is to supply a means of referring to
the taxon, rather than to indicate the characters or history of the taxon.
• The name of a taxon has no official status until it has been approved by
ICTV
124. Rules of Classification and
Nomenclature
• General Rules
• Rules about naming Taxa
• Rules about Species
• Rules about Genera
• Rules about Subfamilies
• Rules about Families
• Rules about Orders
• Rules about Sub-viral Agents
• Rules for Orthography
125. General Rules
• The universal scheme
• Virus classification and nomenclature shall be international and shall
be universally applied to all viruses.
• The universal virus classification system shall employ the
hierarchical levels of Order, Family, Subfamily, Genus, and Species.
• Contrasting examples of full classifications of some
negative strand RNA viruses are:-
• (1) species Mumps virus;
• genus Rubulavirus;
• subfamily Paramyxovirinae;
• family Paramyxoviridae;
• order Mononegavirales, and
• (2) species Rice stripe virus;
• genus Tenuivirus.
126. • The ICTV is not responsible for classification
and nomenclature of virus taxa below the rank of
species.
• The classification and naming of
serotypes, genotypes, strains, variants and
isolates of virus species is the responsibility of
acknowledged international specialist groups.
• Artificially created viruses and laboratory hybrid
viruses will not be given taxonomic
consideration. Their classification will be the
responsibility of acknowledged international
specialist groups.
Scope of the classification
(e.g. peanut stripe virus, which is classified in the species Bean
common mosaic virus, genus Potyvirus, family Potyviridae) or as
serotypes, genotypes, strains, variants, isolates etc. Naming of
such entities is not the responsibility of the ICTV
127. Limitations
• Taxa will be established only when representative
member viruses are sufficiently well characterized and
described in the published literature so as to allow them
to be identified unambiguously and the taxon to be
distinguished from other similar taxa.
• When it is uncertain how to classify a species into a
genus but its classification in a family is clear, it will be
classified as an unassigned species of that family.
• Names will only be accepted if they are linked to taxa at
the hierarchical levels described in Rule 3.2 and which
have been approved by the ICTV.
example, Groundnut rosette assistor virus is classified in the
family Luteoviridae but not within any of the current genera of
that family.
128. II - Rules about naming Taxa
• Names proposed for taxa are "valid names"
• if they conform to the Rules set out in the Code
and they pertain to established taxa.
• Valid names are "accepted names" if they are recorded
as approved International Names in the 8th ICTV Report
or have subsequently become "accepted names" by an
ICTV vote of approval for a taxonomic proposal.
• Existing names of taxa shall be retained whenever
feasible.
• The rule of priority in naming taxa shall not be observed.
• No person's name shall be used when devising names
for new taxa.
129. II - Rules about naming Taxa
• Names for taxa shall be easy to use and easy to remember.
• Euphonious names are preferred.
• Subscripts, superscripts, oblique bars and non-Latin letters may not
be used in taxon names.
• Hyphens should not be used when attaching numbers or letters to
the end of a series of species names and should never be used in
names of genera, subfamilies, families or orders.
• New names shall not duplicate approved names.
• New names shall be chosen such that they are not closely similar to
names that are in use currently or have been in use in the recent
past
• Sigla may be accepted as names of taxa, provided that they are
meaningful to virologists in the field, normally as represented by
Study Groups.
130. II - Rules about naming Taxa
• In the event of more than one candidate name being proposed, the
relevant Subcommittee will make a recommendation to the
Executive Committee of the ICTV, which will then decide among the
candidates as to which to recommend to ICTV for acceptance.
• New names shall be selected such that they, or parts of them, do not
convey a meaning for the taxon which would either
• (1) seem to exclude viruses which lack the character described by
the name but which are members of the taxon being named, or
• (2) seem to exclude viruses which are as yet undescribed but which
might belong to the taxon being named, or
• (3) appear to include within the taxon viruses which are members of
different taxa.
• New names shall be chosen with due regard to national and/or local
sensitivities. When names are universally used by virologists in
published work, these or derivatives shall be the preferred basis for
creating names, irrespective of national origin.
131. Procedures for naming taxa
• All relevant ICTV subcommittees and
study groups will be consulted prior to a
decision being taken on any taxonomic
proposal submitted to the Executive
Committee of the ICTV.
132. III - Rules about Species
• Definition of a virus species
• Species shall be created in
accordance with the following definition:
• A species is the lowest taxonomic
level in the hierarchy approved by the
ICTV.
• A species is a monophyletic group of
viruses whose properties can be
distinguished from those of other species
by multiple criteria.
133. III - Rules about Species
• Construction of a name
• A species name shall consist of as few
words as practicable but be distinct from names
of other taxa.
• Species names shall not consist only of a host
name and the word "virus".
• A species name must provide an
appropriately unambiguous identification of the
species.
134. • A genus is a group of species sharing certain common characters.
• Comment: It is acceptable for a genus to contain a single species.
• A genus name shall be a single word ending in ...virus.
• Approval of a new genus must be accompanied by the approval of a
type species.
V - Rules about Subfamilies
IV - Rules about Genera
A subfamily is a group of genera sharing certain common characters. The
taxon shall be used only when it is needed to solve a complex hierarchical
problem.
Comment: It is acceptable for a subfamily to contain a single genus.
A subfamily name shall be a single word ending in ...virinae.
135. VI - Rules about Families
A family is a group of genera (whether or not
these are organized into subfamilies) sharing
certain common characters.
• Comment: It is acceptable for a family to contain
a single genus.
• A family name shall be a single word ending
in ...viridae.
VII - Rules about Orders
•An order is a group of families sharing certain common characters.
•An order name shall be a single word ending in ...virales.
136. VIII - Rules about Sub-viral Agents
• Viroids
• Rules concerned with the classification of viruses shall also apply to the
classification of viroids.
• The formal endings for taxa of viroids are the word "viroid" for species, the
suffix "-viroid" for genera, the suffix "-viroinae" for sub-families (should this
taxon be needed) and "-viroidae" for families.
• Comment: For example, the species Potato spindle tuber viroid is classified
in the genus Pospiviroid, and the family Pospiviroidae.
• Other sub-viral Agents
• Retrotransposons are considered to be viruses in classification and
nomenclature
• Satellites and prions are not classified as viruses but are assigned an
arbitrary classification as seems useful to workers in the particular fields.
137. IX - Rules for Orthography
• In formal taxonomic usage, the accepted names of virus Orders,
Families, Subfamilies, and Genera are printed in italics and the first
letters of the names are capitalized.
• Comment: See Rule 3.8 for the definition of an "accepted" name.
• Species names are printed in italics and have the first letter of the
first word capitalized. Other words are not capitalized unless they
are proper nouns, or parts of proper nouns.
• Comment: The species names Tobacco mosaic virus and
Murray Valley encephalitis virus are in the correct form and
typographical style. Examples of incorrect forms are Ustilago maydis
virus H (not italicized), Murray valley encephalitis virus (Valley is a
proper noun) or tobacco mosaic virus (not capitalized or italicized).
145. Virosphere
• all those places where viruses are found
or in which they interact with their hosts
• viral world=virosphere
146. • the discovery of giant viruses like
• the mimivirus, isolated from amoeba, which have
a genome larger than some bacteria
• marseillevirus
• mamavirus
• the widespread existence of ‘gene transfer
• agents’ (GTA)-particles mediating genomic DNA
transfer between cells – and their importance in
the bacterial population.
• non-retroviral (non-reverse-transcribing) RNA
virus proteins in eukaryots
Origin of Virosphere
147. Origin of Virosphere
• Aboundenness in environments
• In different water environments the ratio of viral
particles to prokaryotes varies between 5 (in
lakes) and 100 (in deep ocean waters)
• prokaryotes represent 90% of ocean biomass
and viruses 94% of nucleic acid containing
particles
• more than 5,000 viral genotypes or species in
100 L of sea water
• The sequence diversity and uniqueness of viral
metagenomics data– usually about
• 60% (or more) of DNA reads did not encode
proteins that were significantly similar to known
genes
148. Origin of Virosphere
• the diversity and abundance of viruses and the discovery
of viruses carrying proteins from photosynthesis
complexes PSII and PSI have led to the acceptance of
viruses as an important and integral part of the
biosphere
• These new discoveries have led to an intensifying
discussion on the positioning of the viruses (and viral
genes) relative to the tree of life (TOL) and what the
viruses are and what they are not
149. Importance of Virosphere
• contribute to the evolution of protein
domains
• domain transfer or domain exchange
between the virosphere and cells is an
important factor in understanding how
viruses have shaped the evolution of
cellular organisms
150. Importance of Virosphere
• it is a major cause of mortality
• a driver of global geochemical cycles
• a reservoir of the greatest unexplored
genetic diversity on Earth
• a source of a great deal of new knowledge
in the general field of molecular biology
151.
152. Importance of Virosphere in
evolution
• viruses have much faster evolutionary
• rates then their hosts and the sequence
similarity may disappear very quickly
• evolution of viral coding genes is one to
five orders of magnitude faster than their
host
• fast evolving nature is often not taken into
• account in estimating their evolutionary
role
153. Importance of Virosphere in
evolution
• the interference (or overlap) of cellular
• and virosphere structure space based on
common ancestry using th SUPERFAMILY
resource
154. SUPERFAMILY
A resource which uses a library of HMMs
• to assign domains of known structure to
protein sequences
• based on the SCOP classification.
• The SUPERFAMILY database contains the
genomic assignment of SCOP protein
domains
155. SCOP
• The SCOP is a hierarchical classification
of protein structural domains and groups
together those domains which have
structural,
• functional
• and sequence evidence for a common
evolutionary ancestor at the SF level
156. Importance of Virosphere in
evolution
• To
• compare proteins across the full range of
evolutionary distances
• it is necessary to consider SF domains,
the fundamental units of ancestry
157. Importance of Virosphere in
evolution
• SUPERFAMILY release 1.73 (based on SCOP 1.73)
there are
• 1,304 cellular genomes
• 67 archaea;
• 903 bacteria;
• 334 eukaryota
• containing assignments to 1,736 SFs with a significant
• E-value
• viruses do not have a common viral Last Universal
Common Ancestor (LUCA)
158. Importance of Virosphere in
evolution
• when compared to the three superkingdoms
• In the virosphere we found 560 SFs.
• All three superkingdoms share
• SFs with the virosphere and 30-39% of SFs in
different superkingdoms are shared with viruses
• majority of SFs in the virosphere are also found in
cellular organisms,
• 63 SFs are not assigned to any cellular genomes
and thus are virosphere-specific SF (VspSF)