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

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. .

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”.

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.

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.

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

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.

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

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

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

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

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

Viral Size

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

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

Viral Morphology Helical

Viral Morphology Polyhedral Icosahedral

Viral Morphology 3. Enveloped Enveloped Helical Enveloped Polyhedral

Viral Morphology 4. Complex

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

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

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

Viral Replication Bacteriophage 1. Lytic Cycle 2. Lysogenic Cycle

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

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

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

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

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

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

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

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

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

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

Inoculating the allantoic cavity

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 1951 (Cervical Cancer)

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

VIRUS TAXONOMY

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

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.

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

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.

HISTORY AND RATIONALE During the period of 1930-1950 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.

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

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

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

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

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.

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

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)

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.

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

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

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

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.

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. 

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?