VIRUSES

1. 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 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) • protects viral genome from host endonucleases • capsomeres • Binding Sites • Envelope • derived from the host cell • Binding Sites

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

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

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 1951 (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 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.

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