NOMENKLATUR DAN KLASIFIKASI VIRUS

1. NOMENKLATUR DAN KLASIFIKASI VIRUS

2. KLASIFIKASI VIRUS

3. Whatisthepurposeofclassification? • To make structural arrangement for easy comprehension • To communicate taxonomic decisions to the international community of virologist • To enable prediction of properties of new viruses • Possible evolutionary relationships

4. DescriptorsusedinvirusTaxonomy • Virion properties • Morphological properties of virion • Size; Shape; presence or absence of envelop or peplomers; capsomeric symmetry & structure • Physical properties of the virus • Molecular mass • Buoyant density • Sedimentation coefficient • pH stability, Solvent stability, Radiation stability, detergent stability • Cation (Mg2+, Mn2+, Ca2+) stability

5. DescriptorsusedinvirusTaxonomy • Properties of genome • Type of nucleic acid • Strandedness of n/acid • Linear or circular • Sense: +ve or –ve or ambisense • Number of segments • Size of genome or genome segments • Presence or absence and type of 5’ terminal cap • Presence o or absence of5’terminal covalently- linked polypeptide • Presence o or absence of 3’terminal poly (A) tract (or other specific tract) • Nucleotide sequence comparisons

6. Propertiesofprotein DescriptorsusedinvirusTaxonomy • Number; size; functional activities and Amino acid • sequence comparisons • Lipids • Presence or absence; Nature • Carbohydrates • Presence or absence; Nature • Genome organization and replication • Genome organization • Strategy of replication of nucleic acid • Characteristics of transcription • Characteristics of translation and post translational processing • Sites of accumulation of virion proteins, site of assembly site of maturation and release • Cytopathology inclusion body formation

7. DescriptorsusedinvirusTaxonomy • Antigenicproperties • Serological relationship • Mapping epitopes • Biological properties • Host range, natural & experimental; pathogenicity, etiology • Tissue tropism, pathology, histopathology, • Mode of transmission in nature; vector relationship; • Geological distribution

8. Virus Classification Taxonomy from Order downward (three orders now recognized) • Family often the highest classification. Ends in -viridae. • Many families have subfamilies. Ends in -virinae. • Bacterial viruses referred to as bacteriophage or phage (with a few exceptions). Examples • family Myoviridae • genus T4-like phages • type species Enterobacteria phage T4 • family Herpesviridae, subfamily Betaherpesvirinae • genus Muromegalovirus • type species Murine herpesvirus 1

9. Virus Classification I- the Baltimore classification • Was crated by American biologist David Baltimore • It is basically based on the method of viral syntesis • It groups virus into families according to their type of genome • All viruses must produce mRNA, or (+) sense RNA • A complementary strand of nucleic acid is (–) sense • The Baltimore classification has + RNA as its central point • Its principles are fundamental to an understanding of virus classification and genome replication, but it is rarely used as a classification system in its own right

10. Virus Classification I- the Baltimore classification Based on genetic contents and replication strategies of viruses. According to the Baltimore classification, viruses are divided into the following seven classes: 1. dsDNA viruses 2. ssDNA viruses 3. dsRNA viruses 4. (+) sense ssRNA viruses (codes directly for protein) 5. (-) sense ssRNA viruses 6. RNA reverse transcribing viruses 7. DNA reverse transcribing viruses where "ds" represents "double strand" and "ss" denotes "single strand".

13. dsDNA Viruses • No dsDNA virus is known to infect plants • Examples of dsDNA viruses that infect humans • HSV, HPV and adenoviruses • Among the largest known viruses • Genome size varies from 5 to 1180 Kb • Unfragmented genomes • Both linear and circular • Large genome size attributed to stability of dsDNA • Low error rate during replication • Phages are dsDNA viruses (95%)

15. ssDNA Viruses • ssDNA Viruses have the following characteristics • Small genome, 2-7 Kb • Possibly due to unstable nature of ssDNA compared to dsDNA • Circular genomes with the exception of Parvoviridae (hairpin) • No envelope • Predominantly icosahedralcapsids

17. dsRNA Viruses • They utilize RNA dependent polymerase • Icosahedralcapsids • Capsids stays intact inside cell. Why?Genome protection. • Transcription occurs via viral RNA polymerases • Reoviruses (dsRNA) are capable of infecting multiple species (plants, vertebrates, fungi). Not a common phenomenon. • Rhabhoviridae infect multiple species as well • The fact that they carry their own RNA replication/transcription proteins makes them more adept

19. Viruses With + strand RNA Genomes • Very common of plant viruses to be + ssRNA • Only one phage family is + ssRNA • RNA viruses have linear genomes • Similar to ssDNA viruses they are susceptible to nucleases and divalantcation degradation • Coronavirus has the largest genome of + ssRNA virus (16-30 Kb)

21. - ssRNA Viruses • This group includes some of the deadliest viruses • Ebola, rabies, influenza, measles • Only helical nucleocapsids • Nucleocapsid seems to provide stability for RNA dependent RNA polymerase to generate + ssRNA • + ssRNA=mRNA

22. Viruses With ReverseTranscription • 3 families belong to this group • Retroviridae, Ex. HIV • Hepadnaviridae, Ex. Hep B • Caulimoviridae, Ex. Cauliflower Mosaic Virus • These families utilize enzyme that uses an RNA template to make DNA template • Reverse transcriptase is packaged in capsid • Similar to + ssRNA and – ssRNA that package the RNA dependent polymerase • Retroviruses package 2 copies of their RNA genome in the capsid

25. Virus classification II -the Classical system • This is a based on three principles - • that we are classifying the virus itself, not the host • 2) the nucleic acid genome • 3) the shared physical properties of the infectious agent (e.gcapsid symmetry, dimensions, lipid envelope)

26. Virus classification III -the genomic system • More recently a precise ordering of viruses within and between families is possible based on DNA/RNA sequence • By the year 2000 there were over 4000 viruses of plants, animals and bacteria - in 71 families, 9 subfamilies and 164 genera

27. RNA viruses From Principles of Virology Flint et al ASM Press

28. DNA viruses From Principles of Virology Flint et al ASM Press

29. Criteriademarcatingdifferentvirustaxa • Order • Commonpropertiesbetweenseveralfamiliesincluding • Biochemical composition • Viursreplicationstrategy • Particlestructure • Generalgenomeorganization • Family • Commonpropertiesbetweenseveralfamiliesincluding • Biochemical composition • Virusreplicationstrategy • Natureofparticlestructure • Genomeorganization

30. Criteriademarcatingdifferentvirustaxa • Genus • Commonpropertieswithagenus including: • Virus replicationstrategy • Genomesize,organizationand/or numberof segments • Sequencehomologies • Vectortransmission • Species • Commonpropertieswithinaincluding: • Genomerearrangement • Sequencehomologies • Serologicalrelationship • Vector transmission • Hostrange • Pathogenicity • Tissue tropism • Geographical distribution

31. Table 1. Suffixes for taxonomic categories in three codes of nomenclature

33. Criteria for classifying plant virus • Structure of the virus particle • Physicochemical properties particle • Properties of viral nucleic acid • Viral proteins • Serological relationships • Activities in the plant • Methods of transmission

34. The families & genera of viruses infecting plants • Plant viruses are diverse, but not as diverse as animal viruses • Probably because of size constraints imposed by requirement to move through cell to cell of plasmodesmata’s host plants

42. Satellite Viruses Satellite Viruses Viruses that must always be associated with certain typical viruses (helpers) because they depend on the helper for multiplication and plant infections. They often reduce the ability of the helper virus to multiply and cause disease, so the satellite viruses act as parasites. • These viruses require a helper virus • Their genomes encode for capsid proteins • Nucleic acid satellites are either non-coding or encode for non-capsid proteins • Mostly a plant phenomenon • In humans the Hep virus resembles characteristics of satellite virus/viroid

44. INFECTOUS AGENTS • Virion = a complete virus particle, including envelope (if any) • Viroid = an infectious RNA particle, smaller than a virus, lacking a capsid, that causes various plant diseases • Virusoid (satellite RNA) = same as viroid; small, ssRNA molecule, usually 500 to 2000 nucleotides in length, lacking a capsid, lack genes required for the replication virusoid require a helper (satellite) virus to replicate, causes various plant diseases.

45. Example • Viroid • avocado sunblotch viroid, peach latent mosaic, potato spindle tuber, coconut cadang-cadang, tomato plant macho viroid, citrus bent leaf viroid, pear blister canker viroid • Virusoid • - barley yellow dwarf satellite RNA , tobacco ringspot virus satellite RNA Disease Viroid - cause lethal plant diseases; potato spindle tuber disease, chrysanthemum stunt disease, cucumber pale fruit disease, coconut cadang-cadang disease, chrysanthemum stunt disease, tomato apical stunt disease. Virusoid - cause tobacco necrosis

48. PRIONS • A unique infectious agent, protein infectious particle • Prion = a small infectious particle consistingof protein and lack nucleic acid. • Prion – features: • Resistant to inactivation by heating to 90oC, which inactivate virus • The infection is not sensitive to radiation; radiation damages virus genomes • Prions are not destroyed by enzymes that digest nucleic acids • Sensitive to protein denaturing agents; urea, phenol • Prions have direct pairing of amino acids

49. PRIONS • Diseases – • Creutzfeldt-Jakob – mental degeneration, loss of motor function and death (human) • Scrapie and bovine spongiform encephalopathy (BSE) – loss of neuronal function that leads to death in sheep and dairy cattle. • Kuru – a neurological disorder in human Holes brain – “spongiform” Cerebral cortex of a normal human brain (right), patient with CJD (left). Once present in the brain, prions cause normal proteins to refold into abnormal shapes. As these abnormal proteins multiply, they destroy neurons and eventually cause brain tissue to become riddled with holes. Prions can only be destroyed through incineration.

50. Virus, Viroidand Prion • Characteristic between virus, viroid and prion • Nucleic acid type, NA strandedness, host range and structural features