1. Subject: Molecular Virology Instructor: Dr. Sobia Manzoor
VIRUSES
AN INTRODUCTION
Subject: Molecular Virology
Instructor: Dr. Sobia Manzoor
Lecture: 1

2. INTRODUCTION TO VIROLOGY
Virology: study of small biological entities : Viruses
Living organisms: consists either of viruses;
1: Parasites
2: Viral genes incorporated in the genome of a living organism.
Viruses; the smallest of creatures have a great impact on the molecular mechanisms of a living organism.
Since viruses are parasitic in nature therefore the study of viral
genome, viral processes of gene expressions in host cells and
viral replication provides fundamental information regarding the
cellular processes in general. .

3. Viral Entry
Viral Persistence
Pathogenesis of Viral Infections
Host Virus Interactions
Viral Immunopathogenesis
Tumor Biology of Viruses
Definition: Simplest of all definitions quoted by the author S. E. Luria states that “Viruses are submicroscopic entities, capable of being introduced into specific living cells and of reproducing inside such cells only”.

4. Viruses differ from each other on various bases.
They differ on the basis of type of host they infect.
On the other hand viruses they may be distinguished from one another:
Morphology
Genome type or
Mode of replication.

5. There are some unifying principles which all viruses follow:
Viral genome is always packaged inside the core of a particle in order to ensure safe transfer from one host to another
In order to survive, all viruses establish themselves in a host population.
The viral genome consists of all the information required for the initiation and completion of an infectious cycle within a host cell that is rendered susceptible to that specific infection.

6. Study of Viruses - Virology
Five Kingdoms
Plantae
Animalia
Fungi
Protista
Monera

7. Five Characteristics of Life
1. Cells. 2. Grow and maintain their structure by taking up chemicals and energy from the environment. 3. Respond to their external environment 4. Reproduce and pass on their organization to their offspring. 5. Evolve and Adapt to their environment.

8. Viruses are: Acellular. Obligate intracellular parasites.
No ATP generating system.
No Ribosomes or means of Protein Synthesis.

9. Typical Virus Two parts 1. Nucleic Acid 2. Capsid (Coat Protein)
DNA or RNA (But never both)
2. Capsid (Coat Protein)
Some Viruses:
Envelope
Enzymes

10. Host Range Spectrum of host cells that a virus can infect
Some viruses only infect:
Plants
Invertebrates
Protists
Fungi
Bacteria (bacteriophages)

11. Host Range
Most viruses have a narrow host range Polio virus - nerve cells Adenovirus - cells in upper Respiratory Tract

12. Host range is determined by Viruses ability to interact with its host cell
Binding Sites match Receptor Sites
Binding Sites - on viral capsid or envelope
Receptor Sites - on host cell membrane

13. Viral Size

14. Viral Structure 1. Nucleic Acid 2. Capsid (Coat Protein) Nucleic Acid
DNA or RNA (But never both)
ssDNA
ds DNA
ss RNA
ds RNA

15. Viral Structure Capsid (Coat Protein) Envelope
protects viral genome from host endonucleases
capsomeres
Binding Sites
Envelope
derived from the host cell

16. Viral Morphology
Helical

17. Viral Morphology
Polyhedral
Icosahedral

18. Viral Morphology
3. Enveloped
Enveloped Helical
Enveloped Polyhedral

19. Viral Morphology
4. Complex

20. Viral Classification
1. Nucleic Acid 2. Morphology 3. Strategy for replication

21. Viroids and Prions Viroids Naked RNA (no capsid)
300 – 400 nucleotides long
Closed, folded, 3-dimensional shape (protect against endonucleases)
Plant pathogens
Base sequence similar to introns

22. Viroids and Prions Prions Proteinaceous infectious particle 1982
Diseases
Scrapie (sheep)
Creutzfeldt-Jacob disease (CJD)
Kuru (Tribes in New Guinea)
Bovine Spongiform Encephalopathy (BSE)
Mad Cow Disease
CJD – Neurological disorder
Kuru – Transmitted by contact with brain and tissue of dead victims

23. Viral Replication
Bacteriophage
1. Lytic Cycle
2. Lysogenic Cycle

24. Lytic Cycle Attachment
Binding sites must match receptor sites on host cell
2. Penetration
Viral DNA is injected into bacterial cell
3. Biosynthesis
Genome replication
Transcription
Translation
Virus uses Host Cells enzymes and machinery

25. Lytic Cycle
4. Assembly (Maturation) viral particles are assembled 5. Release Lysis

26. Lysogenic Cycle 1. Attachment 2. Penetration 3. Integration
Viral Genome is integrated into Host Cell Genome
Virus is “Latent”
Prophage

27. Lysogenic Cycle 4. Biosynthesis Viral Genome is Turned On
Genome replication
Transcription
Translation
5. Assembly
6. Release
Lysis

29. Animal Virus Replication (non-enveloped virus)
1. Attachment
Binding Sites must match receptor sites on host cell
2. Penetration
Endocytosis (phagocytosis)
3. Uncoating
separation of the Viral Genome from the capsid

30. Animal Virus Replication (non-enveloped virus)
4. Biosynthesis
Genome Replication
Transcription
Translation
5. Assembly
Virus particles are assembled
6. Release/Shedding
Lysis
Buddding
Secretion

31. Enveloped Virus Replication
1. Attachment
2. Penetration
3. Uncoating
4. Biosynthesis
5. Assembly
6. Release
Budding

33. Growing Viruses 1. Bacteriophages Lawn of Bacteria on a Spread Plate
Add Bacteriophages
Infection will result in “Plaques”
Clear zones on plate

34. Growing Viruses 2. Animal Viruses A. Living Animals
mice, rabbits, guinea pigs
B. Chicken Embryos (Eggs)
used to be most common method to grow viruses
Still used to produce many vaccines (Flu Vaccine)
C. Cell Cultures
Most common method to grow viruses today

35. Chick embryonated egg inoculation
Amniotic cavity
Yolk sac
Egg white
Allantoic cavity
Chorioallantoic cavity
Egg membrane
Eggshell
Air sac

36. Inoculating the allantoic cavity

37. Cell Cultures Primary Cell Lines die out after a few generations
Diploid Cell Lines
derived from human embryos
maintained for up to 100 generations
Continuous Cell Lines
Transformed Cells (Cancerous Cells)
may be maintained indefinitly
HeLa Cells
Henrietta Lax (Cervical Cancer)

38. Retro Viruses (1975) Normal Virus Central Dogma of Molecular Genetics
DNA > mRNA > Protein
Retro Virus
RNA > DNA > mRNA > Protein

39. VIRUS TAXONOMY

40. VIRUS TAXONOMY
Traditional tools of taxonomy were not applied to viruses for a long time due to their unique nature
Either ignored since regarded as nonliving entities
Or regarded as similar to the host organism and not among themselves
The development of various similar groups of viruses require deep understanding of these viruses in terms of virus nature and evolution
Virus taxonomy is overseen by the International Committee on Taxonomy of Viruses (ICTV)
With rules and tools unique to the field of virology

41. VIRUS TAXONOMY Evolution of the process of virus taxonomy uses:
Some of the rules of traditional taxonomy
Identifying virus species and grouping them into genera
Genera into families
Families into orders
But at the same time, the classification system has been nonsystematic and based on
“Opinionated usage of data”
Inorder to cope with the uniqueness and diversity of viruses as a group.

42. VIRUS TAXONOMY Importance of virus taxonomy:
Identification of a limited number of biological characteristics e.g
Virion morphology
Genome structure
Antigenic properties, etc
Provide a focus for the identification of an unknown agent for the clinician or epidemiologist
Virus taxonomy is thus an evolving field

43. HISTORY AND RATIONALE Virology as a discipline is only 100 years old
Virus taxonomy is therefore relatively young
In the early 1900’s viruses were classified and distinguished from each other on the basis of some measurable properties such as
Disease or
Symptoms caused in an organism
Thus animal viruses that caused liver pathology were classified as HEPATITIS VIRUSES.
Viruses that caused mottling in plants were generally called MOSAIC VIRUSES.

44. HISTORY AND RATIONALE
During the period of techniques for the study of viruses were developed and thus in the 1950’s the characterizations led to
3 distinct groups of animal viruses
Myxoviruses
Herpesviruses
Poxviruses
But by 1960 it was established that a proper system for the classification of viruses was required
Therefore ICTV (the the International Committee on Nomenclature of Viruses ICNV ) was founded in 1966.

45. HISTORY AND RATIONALE
Most critical issue for virus classification was whether to follow a Monothetic, hierarchical system or a Polythetic, hierarchical system
Monothetic system:
A system based on a single characteristic or a series of single characteristics
Genome structure
Virion symmetry
Polythetic system:
Sharing a number of common characteristics, without any one of these characteristics being essential for membership in the group or class in question
No priority to any one characteristic
But it is almost impossible to systematically take into account all the properties of different viruses
Therefore, a nonsystematic approach is followed

46. HISTORY AND RATIONALE
Using study groups of virologists within the ICTV to consider together numerous characteristics of a virus and make as rational an assignment to a group as possible
Therefore the system that is currently being used is a NONSYSTEMMATIC, POLYTHETIC, HIERARCHICAL system
As a consequence the virus taxonomy of today has been filled initially from the middle
By assigning viruses to genera, and then elaborating the taxonomy upwards by grouping genera into families
And to a limited extent, families into orders

47. HISTORY AND RATIONALE By 1970 the ICTV had established
2 virus families with 2 genera each
24 floating genera, &
16 plant groups
Till date the complete virus taxonomy includes
More than 5450 viruses
3 orders
73 families
9 subfamilies
287 genera
More than 1950 species
A significant number of tentative species

48. BASIS OF CLASSIFICATION
Nucleic acid type Super family
Strand type and sense +/-
Capsid type virion shape
Envelope present or absent
Size
Cell trophism
Persistence
Enzymes in the Virion

49. DIFFERENT SYSTEMS USED FOR THE CLASSIFICATION OF VIRUSES
ICTV classification
Baltimore classification.
Holmes classification.
LHT System of virus classification.
Casjens and Kings classification of virus.

50. ICTV Classification
‘a virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche’
(7th report)
Polythetic class- several properties in common, but not necessarily a single common defining property
Hierarchy of recognised viral taxa:
Order; Family; Subfamily; Genus; Species

52. HOLMES CLASSIFICATION
Holmes (1948) used Carolus Linnaeus system of binomial nomenclature classification system for viruses to group them into 3 groups under one order, Virales. They are placed as follows:
Group I: Phaginae (attacks bacteria)
Group II: Phytophaginae (attacks plants)
Group III: Zoophaginae (attacks animals)

53. LHT System of Virus Classification
The LHT System of Virus Classification is based on chemical and physical characters like
nucleic acid (DNA or RNA),
Symmetry (Helical or Icosahedral or Complex),
presence of envelope,
diameter of capsid,
number of capsomers.

54. LHT System of Virus Classification
This classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of Microbiological Societies (1962). It is as follows:
Phylum Vira (divided into 2 subphyla)
Subphylum Deoxyvira (DNA viruses)
Class Deoxybinala (dual symmetry)
1 order
Class Deoxyhelica (Helical symmetry)
Class Deoxycubica (cubical symmetry)
2 orders
Subphylum Ribovira (RNA viruses)
Class Ribocubica
Class Ribohelica
2 sub orders

55. CASJENS AND KINGS CLASSIFICATION OF VIRUS
Casjens and Kings(1975) classified virus into 4 groups based on type of nucleic acid, presence of envelope, symmetry and site of assembly. It is as follows:
Single Stranded RNA Viruses
Double Stranded RNA Viruses
Single Stranded DNA Viruses
Double Stranded DNA Viruses

56. BALTIMORE CLASSIFICATION
Created by David Baltimore
7 classes
Viruses grouped by type of nucleic acids they possess and its replication scheme.
I. dsDNA viruses
II. ssDNA viruses
III. dsRNA viruses
IV. +ssRNA viruses
V. -ssRNA viruses
VI. RNA reverse transcribing viruses
VII. DNA transcribing viruses

57. Molecular VIROLOGY (HVI-983) Credit Hrs 3 (3-0)
Educational Objectives:
This is an introductory level course that describes the history of virology, development of the concepts of viruses, and various biological and molecular aspects of bacterial, animal and plant viruses. The course is divided into 3 parts.

58. Course Outcomes:
At the end of the course the student will have a good understanding of fundamental concepts of structure and replication of virus. The course will help student to understand fundamental aspects on the effect of virus on eukaryotic and prokaryotic organisms. After reading the course the student will have elaborate knowledge of morphology, taxonomy, mechanisms of replication, strategies of viral gene expression, diseases and biological control of viruses. 

59. Course Contents:
200 years of discoveries
General aspects of virology
Viral Classification and Structure
Modes of infection
Cellular Models of virus propagations
Replication and pathogenesis in a comparative fashion.
Host-virus interactions
Transformation and oncogenesis
Immunopathology
Host defense mechanisms
Antiviral pharmacology and applied virology
Bacteriophages
Plant viruses and their associated diseases
What is next for Virology?