Virology Lecture Material

1. VIROLOGY
MIC 303; C; 2.0
VIRAL TAXONOMY
ANJORIN, A. A.,
Virology & Immunology Research Group,
Department of Microbiology,
Lagos State University, Ojo

2. 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

3.  Our elementary understanding
 Interactive session
 At the end of our discussion, we should all be able to:
1.
2.
3.
INTRODUCTION AND OBJECTIVES

4. 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 )

5.  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

6. 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

7. 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

8. Principles
 ICTV essential principles of virus nomenclature are:
 Stability
 Rejection (prevents confusing names)
 Necessity (avoids unnecessary name creation)

9. 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

10. 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

11. 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

12.  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

13. 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.

14.  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.

15.  VIRINO
-Proteinacious infectious particle i.e. Possess Capsid +
NA together in Association
-N.A. (About 10-12nm)
-Also Non Immunogenic

16.  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

17. VIRAL TAXONOMICAL RULES
 Nomenclature and Classification of viruses do
not Use Conventional Taxonomic Groups
 Suffix ending:
-Viral family
-Sub family
-Order
-Genus

18.  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

19. 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.

20.  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.

21.  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.

22.  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.

23.  Orders
 An order is a group of families sharing certain
common characters.
 An order name must be a single word ending
in virales.

24. CRITERIA FOR VIRAL CLASSIFICATION
 N. A. type
1. DNA
2. RNA viruses

25. 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

26. 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

27. 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

28. 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 )

29. Classification of Viruses based on Genomic composition
and their Pathway of mRNA formation

30. 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

31. Enzyme Components

32. Size and Morphology -Size include:

33. -Morphology

34. 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

35. 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.

36. Host, tissue and Cell tropism

37. Immunological properties
1. Immunogenic
2. Non- Immunogenic viruses e.g.
 Subvirals, etc

38. Pathology
1. Inclusion body formation
2. CPE on Cells e.g. on
 Hela cell, HEP 2, etc
3. Multinucleated Giant Cell producing viruses

39. Symptomatology
1. Koplik spot viruses
2. Haemorrhagic Viruses e.g.
 Rift valley
 CHIK
 DENG
3. Skin Jaundice
4. Salivation

40. Place of first Isolation
 Africa, Asia, etc
 First isolated in Nigeria
 Mokola (Hill, 1970)
 Kotonkanvirus
 Potiskumvirus
 Yabapox (NIMER)
 Igbo-Oravirus

41.  Dugbevirus
 Nairovirus (Nigeria in 1967)
 Ileshavirus
 Lassa virus (NE, 1969)
 Lagos bat virus (LBV)(Eidolon helvum, 1956,
Island)

42. Organism of Natural host
 Ranapox
 Chordopox
 Monkeypox
 Bufallopox

43. Sigla formation Method
 Yatapox (Tanapox, Japan)
 Hepadna
 Papova
 Picorna
 Reo
 Birna

44. After the Researcher who discovered it
 Epstein-Barr virus

45. Presence or Absence of Envelope
 Naked
 Enveloped viruses

47. Taxonomy of Viral Families
A. DNA Viruses
Adenoviridae
(Greek Adenos- Gland)
1. Genus Mastadenovirus
2. Genus Aviadenovirus
 Adenoviruses 1-49
 Human Adenoviruses

48. Baculoviridae
(Latin Baculum-Rod-like)
Virus infects invertebrates
Genus Nucleopolyhedrovirus
Genus Granulovirus

49. Hepadnaviridae
(Sigla, Hepatic- Liver)
Hepatitis B Virus

50. Herpesviridae (Greek Herpes- Creeping)
1. Subfamily Alphaherpesvirinae,
Genera : Simplexvirus, Varicellovirus
2. Subfamily Betaherpesvirinae,
Genera : Cytomegalovirus, Muromegalovirus, Roseolovirus
3. Subfamily Gammaherpesvirinae,
Genera : Lymphocryptovirus, Rhadinovirus
Unclassified 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)

51. 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)

52. Papovaviridae
(Sigla, Old and discontinued family, Now divided)

53. Papillomaviridae
(Warts and Condylomas-
M. Membrane)
Sixteen Genera:
HPV
Bovine PV, etc

54. Parvoviridae
(Greek Parvus- Small)
2 subfamilies:
I. Parvovirinae (Five Genera):
 Parvoviruses
(Animal, Canine Parvoviruses)
 Erythroviruses (B19)
 Dependoviruses
 Amdoviruses
 Betaparvoviruses
II. Densovirinae
Invertebrates

55. Plasmaviridae
(Greek Plasma- Shaped product)
 Mycoplasma

56. Poxviridae
(Greek Poc/ Pocc- Pustule)
Subfamily Chondropoxvirinae
Subfamily Entomopoxvirinae
Unclassified viruses
Smallpox Virus
Vaccinia Virus
Monkeypox and Bufallopox
Molluscum Contagiosum Virus

57. 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

58. Others DNA Viruses
 Ds non enveloped
 Caulimoviridae
 Myoviridae
 Phycodnaviridae
 Tectiviridae
 Ss non enveloped
 Circoviridae

59. B. RNA VIRUSES
Arenaviridae
(Latin: Arenosus- Sandy)
Genus Arenavirus
A. 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

60. Astroviridae
(Greek Astron- Star-like)
Genus Astrovirus
Human Astroviruses

61. Birnaviridae
(Sigla, Bi-Double Stranded genome).
Three Genera affecting fish, chickens and insects:
 Aquabirnavirus
 Avibirnavirus
 Entomobirnavirus

62. Bornaviridae
 Genus Bornavirus
 Borna Disease Virus

63. Bunyaviridae
(Bunyamwera, Uganda)
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

64. Caliciviridae
(Greek Calix- Cup)
Hepatitis E Virus
(Provisional)
Human Caliciviruses

65. Coronaviridae
(Greek Corona- Crown/
Petal- like)
Genus Torovirus
Genus Coronavirus
e.g. Human Coronavirus-
SARS Virus

66. Cystoviridae
ds positive non
segmented enveloped
Genus Cystovirus
e.g.
Pseudomonas syringae
phage phi6

67. Filoviridae
(Greek Filo- Thread-like)
Order Mononegavirales
Genus Filovirus
Ebola Virus
(Ebola river in Zaire, 1976)
Marburg Virus
(1st, Lab Workers in Europe,
1967)

68. A. BSL4 B. KITTING

69. 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 Virus
West Nile Virus (Uganda West Nile
District )
Potiskum Virus (Mice, 1969)
Zika Virus (Uganda Zika forest
Monkey, 1947, Also Nigeria)

70. Orthomyxoviridae
(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

71. Paramyxoviridae (Greek Para- By the side of; Myxo-)
Two Subfamilies:
1. Pneumovirinae
Respiratory Syncytial
Virus
2. Paramyxovirinae
Genus Paramyxovirus
e.g. Human paramyxovirus
and H parainfluenza 1

72. Contd.: Paramyxoviridae
Genus Morbilivirus e.g.
Measles Virus
Genus Rubulavirus e.g.
Mumps Virus

73. Picornaviridae
(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
Encephalomyocarditis virus
5. Genus Aphthovirus
Foot and Mouth Disease V.

74. Reoviridae (Sigla, R.E.O. ).
Four Genera- Medicals.
Genus Orthoreovirus- Human
Reovirus
Genus Rotavirus- Human rota
Genus Coltivirus- Colorado
Tick fever Virus
Genus Orbivirus-Orungo V.
Others
Aquareovirus
Cypovirus e.g. Cypovirus type
1-12
Fijivirus, etc

75. 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)

76. Retroviridae (Sigla, Reverse transcriptase)
Subfamilies: Oncovirinae,
Lentivirinae, Spumavirinae
Seven Genera
1. Genus Gammaretroviruses
2. Genus Episilonretroviruses
3. Genus Alpharetroviruses
4. Genus Betaretrovirus group
5. Genus Deltaretroviruses
6. Genus Lentivirus e.g.
HIV
Human T- Leukaemia Virus
Type 1 and 2
7. Genus Spumavirus

77. Rhabdoviridae
(Greek Rhabdo-Straight
bullet- shaped)
Genus Vesiculovirus e.g.
Rhabdovirus
Genus Lyssavirus e.g.
Rabies Virus
Mokola Virus
Genus Ephemerovirus
Others

78. Togaviridae
(Latin Toga- Mantle or Cloak, A
Cover/ layer) because the virions are
surrounded by a lipid envelope and
haemagglutinin spikes
1. Genus Alphavirus
SFV
Chikungunya Virus
Igbo-Ora Virus; Sindbis virus
2. Genus Rubivirus
Rubella (from latin word- little red)
Virus (German measles)
Only virus of the Genus

79. Toroviridae
(Latin Torus- Lowest Convex)
 Some consider Torovirus as a Genus in the family
Coronaviridae
 Human toroviruses

80. Others RNA Viruses
 Non enveloped
 Potyviridae

81. 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

82. 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
 ?

83. Classification of Subviral agents
 1. FAMILY DELTAVIRIDAE
 2. SLOW VIRUSES

84. 1. FAMILY DELTAVIRIDAE
-One Genus: Deltavirus
-Contains Hepatitis D virus a.k.a Delta agent
-A defective RNA virus, replicates in HBV infected
hepatocytes

85. 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)

86. Thank you all.

87. 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

88.  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_Taxonom
y_of_Viruses