VIROLOGY MIC 303; C; 2.0 VIRAL TAXONOMY ANJORIN, A. A., Virology & Immunology Research Group, Department of Microbiology, Lagos State University, Ojo
May 10, 2015
VIROLOGY MIC 303; C; 2.0
VIRAL TAXONOMYANJORIN, A. A.,
Virology & Immunology Research Group,
Department of Microbiology,
Lagos State University, Ojo
OUTLINE
Introduction and Objectives Definitions Principles of Viral Taxonomy Rules Criteria for Viral Classification Viral families Family of Subviral Agent Classical Examples Summary Further studies
Our elementary understanding Interactive session At the end of our discussion, we should all be able to:
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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
information 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
ICTV. http://talk.ictvonline.org 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-year intervals
Objectives
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
Principles
ICTV essential principles of virus nomenclature are:
Stability Rejection (prevents confusing
names) Necessity (avoids unnecessary name
creation)
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: 6 Order 94 families ( > 24 families cause disease in human) 22 Sub families 395 Genera 2,480 Species
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 single property-and virus groups in different branches of the taxonomy can be characterized by different collections of properties
BASIC TERMS IN VIRAL TAXONOMY
VIRION Entire infectious viral particle in nature VIROID- 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.
VIRUSOIDS-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 protein
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.
VIRINO-Proteinacious infectious particle i.e.
Possess Capsid + NA together in Association
-N.A. (About 10-12nm)-Also Non Immunogenic
VIROPLASM-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 SATELLITE VIRUS
-A defective virus-Depends on helper virus for its replication. DEFECTIVE VIRUS- A virus which is unable to replicate because it
lacks a complete genome
VIRAL TAXONOMICAL RULES
Nomenclature and Classification of viruses do not Use Conventional Taxonomic Groups
Suffix ending:-Viral family-Sub family-Order-Genus
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 mRNA.
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
Species 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 used.
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.
Genera 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.
Subfamilies A subfamily is a group of genera sharing
certain common characters. Taxon shall be used only when it is
needed to solve a complex hierarchical problem.
A subfamily name must be a single word ending in virinae.
Families A family is a group of genera, whether or
not these are organized into subfamilies, sharing certain common characters.
A family name must be a single word ending in viridae.
Orders An order is a group of families sharing
certain common characters. An order name must be a single word
ending in virales.
CRITERIA FOR VIRAL CLASSIFICATION
N. A. type
1. DNA
2. RNA viruses
Nature and Strandedness
Nature can be:
Linear/ Circular
Segmented/ Non segmented genome or
Based on Polarity.
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)
Baltimore’s work:
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 RNA
+) And there is also ss RNA that is negative known as (ss RNA –ve)
(Abnormal )
Classification of Viruses based on Genomic composition and their Pathway of mRNA formation
Enzyme possession
Reverse transcriptase 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
Polymerase enzymes
-RNA-dependent RNA polymerase in RNA viruses
-DNA polymerase in smallpox virus
-RNA-dependent DNA polymerase (Reverse transcriptase) in hepatitis B viruses and retroviruses
Enzyme Components
Size and Morphology -Size include:
-Morphology
Susceptibility to Physical and Chemical Agents
Heat (50- 60o C; 30 min. death) and Cold (+4, -20, -60, -80, -196 LN, -252 LH)
Room temperature +15 to +30 Refrigeration +2 to +8 Frozen -5 to -25 Ultra -68 to -85 LN-190 Virucidals: Hypochlorite, Isopropanol, Ether, O.As
(H2O2) Chemotherapeuticals
-Not antibiotic (Viral purification)
-Nucleotide Analogues- Polyomavirus-Nucleoside Analogues- HIV, Lassa
Mode of transmission
1. Respiratory route viruses Influenza Measles viruses, e.t.c.
2. Transovarian (infected sperm to embryo) route viruses e.g.
Cytomegalovirus HIV-1, e.t.c.
Host, tissue and Cell tropism
Immunological properties
1. Immunogenic2. Non- Immunogenic viruses e.g.
Subvirals, etc
Pathology
1. Inclusion body formation2. CPE on Cells e.g. on Hela cell, HEP 2, etc 3. Multinucleated Giant Cell producing
viruses
Symptomatology
1. Koplik spot viruses2. Haemorrhagic Viruses e.g. Rift valley CHIK DENG3. Skin Jaundice4. Salivation
Place of first Isolation
Africa, Asia, etc First isolated in Nigeria
Mokola (Hill, 1970) Kotonkanvirus Potiskumvirus Yabapox (NIMER) Igbo-Oravirus
Dugbevirus Nairovirus (Nigeria in 1967) Ileshavirus Lassa virus (NE, 1969) Lagos bat virus (LBV)(Eidolon
helvum, 1956, Island)
Organism of Natural host
Ranapox Chordopox Monkeypox Bufallopox
Sigla formation Method
Yatapox (Tanapox, Japan) Hepadna Papova Picorna Reo Birna
After the Researcher who discovered it
Epstein-Barr virus
Presence or Absence of Envelope
Naked Enveloped viruses
Taxonomy of Viral FamiliesA. DNA Viruses
Adenoviridae(Greek Adenos-
Gland)
1. Genus Mastadenovirus
2. Genus Aviadenovirus
Adenoviruses 1-49 Human
Adenoviruses
Baculoviridae
(Latin Baculum-Rod-like)
Virus infects invertebrates
Genus NucleopolyhedrovirusGenus Granulovirus
Hepadnaviridae
(Sigla, Hepatic- Liver)
Hepatitis B Virus
Herpesviridae (Greek Herpes- Creeping)
1. Subfamily Alphaherpesvirinae, Genera : Simplexvirus, Varicellovirus2. Subfamily Betaherpesvirinae,Genera : Cytomegalovirus, Muromegalovirus, Roseolovirus3. Subfamily Gammaherpesvirinae,Genera : Lymphocryptovirus, RhadinovirusUnclassified viruses: 48 known.Genus Human Herpes Virus (HHV):HHV- 1 (Herpes Simplex Virus 1)HHV- 2 (Herpes Simplex Virus 2)HHV- 3 (Varicella Zoster Virus)HHV- 4 (Epstein- Barr Virus)HHV- 5 (Cytomegalovirus)HHV- 6 (Herpes Lymphotropic Virus)HHV- 7 (Human Herpes Virus 7)HHV- 8 (Kaposi)
Iridoviridae
(Word Iridescent, Many bright colour, Changes in light).
Four Genera:
Iridovirus (Arthropods, type species: Invertebrate iridescent virus 6)
Chloriridovirus ( Also, Insects) Ranavirus Lymphocystivirus (fish)
Papovaviridae
(Sigla, Old and discontinued family, Now divided)
Papillomaviridae
(Warts and Condylomas- M. Membrane)
Sixteen Genera:
HPVBovine PV, etc
Parvoviridae
(Greek Parvus- Small)2 subfamilies:I. Parvovirinae (Five
Genera): Parvoviruses(Animal, Canine
Parvoviruses) Erythroviruses (B19) Dependoviruses Amdoviruses BetaparvovirusesII. DensovirinaeInvertebrates
Plasmaviridae
(Greek Plasma- Shaped product)
Mycoplasma
Poxviridae
(Greek Poc/ Pocc- Pustule)
Subfamily ChondropoxvirinaeSubfamily EntomopoxvirinaeUnclassified viruses
Smallpox VirusVaccinia VirusMonkeypox and BufallopoxMolluscum Contagiosum Virus
Polyomaviridae
(Greek Poly- many, oma- Cancer)
BK Virus (BKV) JC Virus (JCV) Simian Virus (Monkey) Bovine polyoma virus Mouse polyoma virus Rat polyoma virus, etc
Others DNA Viruses
Ds non enveloped Caulimoviridae Myoviridae Phycodnaviridae Tectiviridae
Ss non enveloped Circoviridae
B. RNA VIRUSES
Arenaviridae (Latin: Arenosus- Sandy)Genus ArenavirusA. Subgroup Tacaribe Complex(New world arenaviruses)Lymphocytic Choriomeningitis V.B. Subgroup LCM-LASV Complex(Old world arenaviruses) Lassa Fever Virus Sabia Virus Guanarito Virus Machupo Virus
Astroviridae
(Greek Astron- Star-like)
Genus AstrovirusHuman Astroviruses
Birnaviridae
(Sigla, Bi-Double Stranded genome).
Three Genera affecting fish, chickens and insects:
Aquabirnavirus Avibirnavirus Entomobirnavirus
Bornaviridae
Genus Bornavirus Borna Disease Virus
Bunyaviridae
(Bunyamwera, Uganda)Seven groups (19 viruses) and22 ungrouped viruses:
Genus Bunyavirus e.g. Bunyamwera, La Cross virus
Genus Hantavirus e.g. Hantaan Genus Phlebovirus e.g. Rift VFVGenus Nairovirus e.g. Crimean- Congo Haemorrhagic Fever Virus
Caliciviridae
(Greek Calix- Cup)
Hepatitis E Virus (Provisional)
Human Caliciviruses
Coronaviridae
(Greek Corona- Crown/ Petal- like)
Genus Torovirus
Genus Coronavirus e.g. Human Coronavirus-SARS Virus
Cystoviridae
ds positive non segmented enveloped
Genus Cystoviruse.g.Pseudomonas syringae phage phi6
Filoviridae
(Greek Filo- Thread-like)Order Mononegavirales
Genus Filovirus
Ebola Virus(Ebola river in Zaire, 1976)Marburg Virus(1st, Lab Workers in Europe, 1967)
A. BSL4 B. KITTING
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 Dengue VirusWest Nile Virus (Uganda West Nile District )Potiskum Virus (Mice, 1969)Zika Virus (Uganda Zika forest Monkey, 1947, Also Nigeria)
Orthomyxoviridae
(Greek Ortho-Straight, Myxo- Mucous)Surface projections of envelope distinct; About 500 spikes8 gene segments (PB1, PB2, PA, HA, NP, NA, M, NS).
-Epidemics and pandemics by Antigenic Drift (accumulation of point mutations=Gradual changes) andShift (major antigenic changes=new subtype into human population).1. Genus Influenzavirus A2. Genus Influenzavirus B3. Genus Influenzavirus C4. Genus Thogoto-like Viruses
Paramyxoviridae (Greek Para- By the side of; Myxo-)
Two Subfamilies:
1. PneumovirinaeRespiratory Syncytial Virus2. Paramyxovirinae
Genus Paramyxoviruse.g. Human paramyxovirusand H parainfluenza 1
Contd.: Paramyxoviridae
Genus Morbilivirus e.g. Measles Virus
Genus Rubulavirus e.g. Mumps Virus
Picornaviridae
(Sigla, Greek Pico- Small)1. Genus Enterovirus e.g. Enteroviruses 68, 70, 71Polio Virus and Coxsackie2. Genus RhinovirusHuman rhinovirus 1A3. Genus Hepatovirus Human hepatitis A virus4. Genus CardiovirusEncephalomyocarditis virus5. Genus AphthovirusFoot and Mouth Disease V.
Reoviridae (Sigla, R.E.O. ).
Four Genera- Medicals.Genus Orthoreovirus- Human ReovirusGenus Rotavirus- Human rotaGenus Coltivirus- Colorado Tick fever VirusGenus Orbivirus-Orungo V.OthersAquareovirusCypovirus e.g. Cypovirus type 1-12Fijivirus, etc
Genus Rotavirus
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 and VP7 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)
Subfamilies: Oncovirinae, Lentivirinae, SpumavirinaeSeven Genera1. Genus Gammaretroviruses2. Genus Episilonretroviruses3. Genus Alpharetroviruses4. Genus Betaretrovirus group5. Genus Deltaretroviruses
6. Genus Lentivirus e.g.HIVHuman T- Leukaemia Virus Type 1 and 27. Genus Spumavirus
Rhabdoviridae
(Greek Rhabdo-Straight bullet- shaped)Genus Vesiculovirus e.g. Rhabdovirus
Genus Lyssavirus e.g.Rabies VirusMokola Virus
Genus EphemerovirusOthers
Togaviridae
(Latin Toga- Mantle or Cloak, A Cover/ layer) because the virions are surrounded by a lipid envelope and haemagglutinin spikes1. Genus AlphavirusSFVChikungunya VirusIgbo-Ora Virus; Sindbis virus2. Genus RubivirusRubella (from latin word- little red) Virus (German measles)Only virus of the Genus
Toroviridae
(Latin Torus- Lowest Convex)
Some consider Torovirus as a Genus in the family Coronaviridae
Human toroviruses
Others RNA Viruses
Non enveloped Potyviridae
TAXONOMY OF SUBVIRAL AGENTS
-Taxonomical Properties of subviral agents include:i. No Genomeii. No I.R.iii. Filterable sizeiv. No inactivation by heat, disinfectant and UV lightv. Tend to be modified human protein that is infectiousvi. Usually tend to form insoluble aggregate of fibrilsvii. 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 hepatocytes
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
Encephalopathy)
Thank you all.
FURTHER READING
Anjorin, A. A., Omilabu, S. A., Salu, O. B., Oke, B. O. (2012). Detection of Influenza A virus in Pigs in Lagos, Nigeria. Afr. J. Cln. Exper. Microbiol, 13(1): 41-45. http://dx.doi.org/10.4314/ajcem/v13i1
Brooks, GF, Carol, KC, Butel, JS, Morse, SA. (2007). Selected Medically Important Microorganisms. Viruses. In: Jawetz, Melnick and Adelberg’s Medical Microbiology. Mc Graw Hill, New York.
Cheesbrough M. (2002). District Laboratory Practice in Tropical Countries Part 2. Cambridge University Press, UK
El-Azizi, M. Lecture 1 General virology. Fagbami AH (2008). Medical Virology Lecture Supplements.
Nihinco Prints Mokola, Ibadan. Knipe, D. M. and Howley, P. M. (2007). Fields Virology. Vol. 1.
5th Edition. Lippincott Williams & Wilkins
Lodish H, Berk A, Zipursky SL, et al., (2000). Molecular Cell Biology. 4th edition. Freeman and Company, New York:
Mahy, B.W.J. (2009). The Dictionary of Virology. Fourth Edition. Academic Press, UK
Oyefolu, A. O. B. (2008). Unpublished Virology Lecture Series. Department of Microbiology, LASU, Lagos.
Obayori, O. S. (2008). Unpublished Virology Lecture Series. Department of Microbiology, LASU, Lagos.
Sander, D. (2007). The Big Picture Book of Viruses. http://www.virology.net/big_virology/BVFamilyGenome.html
Wikipedia (2012). ICTV. http://en.wikipedia.org/wiki/International_Committee_on_Taxonomy_of_Viruses