VIRUS STRUCTURE AND CLASSIFICATION

1. VIRUS STRUCTURE AND CLASSIFICATION Claude MUVUNYI M.D., Ph.D.

2. Terminology In 1962, Caspar et al. defined the following terms: • Virion: The complete infectious virus particle. • Capsid: The protein coat that surrounds nucleic acid. • Nucleocapsid: The nucleic acid plus the capsid. • The nucleocapsid may be enclosed inside an ENVELOPE containing proteins encoded by the virus. • STRUCTURE UNITS are the smallest equivalent building units of the capsid. • Capsomeres: The structural protein units that made up the capsid.

3. General structure of viruses • Viruses composed of nucleic acid either DNA or RNA, surrounded by a protein coat called the capsid. • The capsid is composed of small structural units called capsomeres. • The capsid protects nucleic acid from inactivation by the outer physical conditions. • Some viruses have additional lipoprotein envelope , composed of virally coded protein and host lipid. The viral envelope is covered with glycoprotein spikes.

4. General structure of viruses • Some viruses have enzymes inside the virion. All ss- RNA viruses with negative polarity have the enzyme transcriptase ( RNA dependent RNA polymerase) inside virions.

5. Virus Shapes

6. General morphology Viruses may be classified into several morphological types on the basis of their capsid architecture as revealed by electron microscopy and a technique called x-ray crystallography.

7. Virus structure • Self assembly of virus capsids follows two basic patterns: • Helical symmetry, in which the protein subunits and the nucleic acid are arranged in a helix. • Icosahedral symmetry, in which the protein subunits assemble into a symmetric shell that covers the nucleic acid-containing core.

8. Virus structure • Larger viruses often have a complex architecture consisting of both helical and isometric symmetries confined to different structural components. • Small viruses, e.g., hepatitis B virus or the members of the picornavirus or parvovirus family, are orders of magnitude more resistant than are the larger complex viruses, e.g. members of the herpes or retrovirus families.

9. DNA or RNA Basic virus structure Capsid protein Naked capsid virus Nucleocapsid + = Lipid membrane, glycoproteins Nucleocapsid Enveloped virus +

10. Matrix Lipid Glycoprotein Capsid symmetry Icosahedral Helical Naked capsid Enveloped

11. Adenovirus Electron micrograph Foot and mouth disease virus Crystallographic model Icosahedral naked capsid viruses http://virology.wisc.edu/virusworld/ICTV8/fmd-foot-and-mouth-ictv8.jpg http://www.ncbi.nlm.nih.gov/ICTVdb/Images/Ackerman/Animalvi/Adenovir/799-16.htm

12. Helical naked capsid viruses RNA Protein http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/em_tmv.gif Caspar and Klug, Adv Virus Res. 1960;7:225-325 Tobacco mosaic virus Electron micrograph Tobacco mosaic virus Model

13. Icosahedral enveloped viruses http://web.uct.ac.za/depts/mmi/stannard/emimages.html http://virology.wisc.edu/virusworld/images/herpescapsid.GIF Herpes simplex virus Electron micrograph Herpes simplex virus Nucleocapsid cryoEM model

14. Helical enveloped viruses http://web.uct.ac.za/depts/mmi/stannard/fluvirus.html http://web.uct.ac.za/depts/mmi/stannard/paramyx.html Influneza A virus Electron micrograph Paramyxovirus Electron micrograph

15. Properties of enveloped viruses • Envelope is sensitive to • Drying • Heat • Detergents • Acid • Consequences • Must stay wet during transmission • Transmission in large droplets and secretions • Cannot survive in the gastrointestinal tract • Do not need to kill cells in order to spread • May require both a humoral and a cellular immune response Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA Box 6-5

16. Properties of naked capsid viruses • Capsid is resistant to • Drying • Heat • Detergents • Acids • Proteases • Consequences • Can survive in the gastrointestinal tract • Retain infectivity on drying • Survive well on environmental surfaces • Spread easily via fomites • Must kill host cells for release of mature virus particles • Humoral antibody response may be sufficient to neutralize infection Adapted from Murray, P.R. Rosenthal K.S., Pfaller, M.A. (2005) Medical Microbiology, 5th edition, Elsevier Mosby, Philadelphia, PA , Box 6-4

17. FIVE BASIC STRUCTURAL FORMS OF VIRUSES IN NATURE • Naked icosahedral e.g. poliovirus, adenovirus, hepatitis A virus • Naked helical e.g. tobacco mosaic virus. So far no human viruses with this structure are known • Enveloped icosahedral e.g. herpes virus, yellow fever virus, rubella virus • Enveloped helical e.g. rabies virus, influenza virus, parainfluenza virus, mumps virus, measles virus • Complex e.g. poxvirus

18. CLASSIFICATION OF VIRUS

19. Naming of Viruses Usually based on data available when a virus is discovered: • Diseases viruses are associated with, e.g.: Poxvirus, Hepatitis virus, HIV, Measles virus. • Cytopathology occuring during infection, e.g.:Respiratory Syncytial virus, Cytomegalovirus. • Site of infection, e.g.: Adenovirus, Enterovirus, Rhinovirus, Enterovirus. • Places where viruses were found or people who discovered them, e.g.:Epstein-Barr virus, Rous Sarcoma, Rift Valley Fever. • Biochemical features, e.g.: Retrovirus, Picornavirus Such names are not useful for orderly classification!!!!

20. Enterically transmitted “Infectious” A E F, G, ? Other * Viral hepatitis NANB Parenterally transmitted “Serum” B C D These naming conventions can lead to confusion later e.g.:viral hepatitis is caused by at least 6 different viruses * 10-20% of cases of presumed viral hepatitis are still not accounted for.

21. Related Herpesviruses Cause Many Different Diseases • HSV Herpes Simplex Virus Cold sores (type 1), Genital lesions (type 2) • VZV Varicella Zoster Virus Chicken pox • CMV Cytomegalovirus Mononucleosis • EBV Epstein-Barr Virus Mononucleosis,Burkitt’s lymphoma, • Nasopharyngeal carcinoma • and HHV-6, HHV-7, HHV-8….. (Human HerpesVirus-#) Therefore if these viruses were classified based on their symptoms their relationships would be missed.

22. Thus, Different viruses can cause (nearly) the same symptoms. e.g., thehepatitis viruses However, different members of the same group can cause different symptoms. e.g., theherpes viruses So virologists had to devise more orderly schemes for classification

23. Meeting Classification Needs • A universal system of viral classification and a unified taxonomy was established by the International Committee on Taxonomy of Viruses (ICTV) in 1966. The system makes use of a series of ranked taxons, with the: • - Order (-virales) being the highest currently recognized. • - then Family (-viridae) • - Subfamily (-virinae) • - Genus (-virus) • - Species ( eg: tobacco mosaic virus) By the year 2000, over 4000 viruses of plants, animals and bacteria had been included in 71 families, 9 subfamilies and 164 genera. The ICTV seeks input from a wide range of virologists and meets every three years to revise the taxon.

24. The most important characters are at the top of the Scheme. Other characters are ranked below in order of importance. This scheme brings order to the classification of viruses irrespective of their hosts or disease symptoms Poxviridae Herpesviridae Retroviridae Picornaviridae ICTV Classification Uses a Hierarchical Scheme (Suffix: viridae) (Suffix: virinae) (Suffix: virus)

25. Primary characteristics used in classification Viruses are classified according to the nature of their genome and their structure

26. Genetic material Is Most Important!!! • form of nucleic acid • ssDNA(+ or - strand) • dsDNA • ssRNA(+ or - strand) • dsRNA • segmented RNA • genetic organization • sequence homology • DNA sequence • Hybridization • Morphology: by electron microscopy

27. Secondary characteristics Replication strategy • Sometimes a group of viruses that seems to be a single group by the above criteria is found to contain a subgroup of viruses which have a fundamentally different replication strategy – • In this case the group will be divided based on the mode of replication.

28. David Baltimore’s viral genome classification scheme Genomes and strategies of replication most important features for classification. Baltimore originally proposed six different major categories: Class I:Viruses with double strand DNA genomes. (Adenoviruses) Class II:Viruses with single strand DNA genomes. (Geminiviruses) Class III:Viruses with double strand RNA genomes. (Reoviruses) Class IV:Plus-sense RNA Viruses. (Picornaviruses) Class V:Viruses with Negative strand RNA genomes. (Rhabdoviruses) Class VI:Viruses with Reverse transcribed RNA genomes. (Retroviruses) We can now add a Seventh Genome Class. Class VII:DNA Genomes replicated by reverse transcription. (Hepatitis B like Pararetroviruses)

29. RNA Virus Families • Several general features are evident from the classification: • None of the dsRNA viruses are enveloped. • The minus-strand viruses are enveloped with helical nucleocapsids. • Most of the plus-strand strand viruses have icosahedral nucleocapsids. • Plus strand viruses vary in having envelopes. • Most of the plus strand viruses have a single genomic RNA.

30. DNA Viruses DNA Viruses differ in many features from RNA Viruses: Only three families are enveloped. All families except for the poxviruses replicate in nuclei. Many families have very complex nucleocapsids.