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:

1.

2.

3.

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