Chapter 2 viral structure and classification.pptx

virology lecture

1. CHAPTER 2 VIRUS STRUCTURE AND CLASSIFICATION Essential Human Virology, 2 nd Edition

2. Following completion of this chapter, students should be able to : Explain the general properties of viruses; Reconstruct the architecture of helical and icosahedral viruses, identifying the components and viral proteins involved; Explain how viruses are classified and named. Learning Objectives

3. Lecture Outline

4. 1. Viruses are small in size: Human viruses can vary in size but are generally in the range of 20-200 nm in diameter. In comparison, bacteria are generally 2-3 µM in length, and an average human cell is 10-30 µM . The Properties of Viruses Figure 2.1

5. 2. Viruses are obligate intracellular parasites, they are completely dependent upon the internal environment of the cell to create new infectious virus particles, or virions. 3. Viral genomes can be DNA or RNA Double-stranded (ds) or single-stranded (ss) Genome size can vary; typically 7-20 kb Herpesviruses: 200+ kb Pandoraviruses; 2.5 mb! Smallest eukaryotic genome, parasite Encephalitozoon. intestinalis : 2.2 mb Human cell: ∼3 gb Largest known genome, flowering plant Paris japonica : 150 gb The Properties of Viruses

6. Basic virion structure The Structure of Viruses Figure 2.1 Viral capsid proteins protect the fragile genome, composed of nucleic acid, from the harsh environment. The capsid and nucleic acid together are known as the nucleocapsid .

7. Basic virion structure: naked (non-enveloped) versus enveloped virus The Structure of Viruses Figure 2.3 The capsid of an enveloped virion is wrapped with one or more lipid membranes derived from the cell. Virus attachment proteins located in the capsid or envelope facilitate binding of the virus to its host cell.

8. The Structure of Viruses: Helical and Icosahedral Shapes Helical structure Figure 2.4 A) Viral capsid proteins wind around the nucleic acid, forming a helical nucleocapsid. B) Helical structure of tobacco mosaic virus. Rendering of 49 subunits was performed using QuteMol (IEEE Trans Vis Comput Graph 2006; 12: 1237–44) using a 2xea PDB assembly (J Struct Biol 2010; 171: 303–8).

9. Helical structure The Structure of Viruses: Helical and Icosahedral Shapes Amplitude (diameter) Pitch (height of one turn) A helix is mathematically defined by two parameters: One is the Amplitude of the helix. This is simply the diameter of the helix. The other is the PITCH of the helix. This is how much distance is traveled in one revolution of the helix. AMPLITUDE = DIAMETER PITCH = HEIGHT OF ONE TURN

10. Helical structure The Structure of Viruses: Helical and Icosahedral Shapes Pitch (height of one turn) 1 foot Pitch = rise x number P = m x p How do we figure out Pitch? Pitch = P The PITCH can be figured out by multiplying the NUMBER of subunits in a turn (p) by the RISE of each subunit (how much distance is gained by each subunit) ( m ) P = p x m

11. Helical structure The Structure of Viruses: Helical and Icosahedral Shapes Question: Figure out the Pitch of Tobacco Mosaic Virus, a helical virus. p (subunits / turn of the helix): 16.3 m (rise of each subunit): 0.14nm P = p x m P = 16.3 x 0.14nm P = 2.28nm Tobacco mosaic virus USDA Beltsville EM Unit

12. Helical structure The Structure of Viruses: Helical and Icosahedral Shapes Vesicular stomatitis virus CDC/Dr. Fred A. Murphy Ebola virus CDC/Cynthia Goldsmith Figure 2.5 Electron Micrographs of Helical Viruses. A) Vesicular stomatitis virus forms bullet-shaped helical nucleocapsids. Image courtesy of CDC/ Dr. Fred A. Murphy. B) Tobacco mosaic virus forms long helical tubes. Image courtesy of the USDA Beltsville Electron Microscopy Unit. C) The helical Ebola virus forms long threads that can extend over 1000 nm in length. Image courtesy of CDC/Cynthia Goldsmith.

13. Helical structure Can be enveloped or naked (non-enveloped) Most plant viruses are helical Very uncommon that they are enveloped In contrast, all helical animal viruses are enveloped Viruses can have helical virion structure (rabies virus, Ebola virus) or can have helical nucleocapsids inside a spherical envelope (influenza virus, measles virus) The Structure of Viruses: Helical and Icosahedral Shapes

14. Icosahedral structure: More prevalent than helical architecture 20 faces composed of equilateral triangles The Structure of Viruses: Helical and Icosahedral Shapes Figure 2.6 This is an icosahedron. Any idea how many sides an icosahedron has?

15. Icosahedral structure: More prevalent than helical architecture 20 faces composed of equilateral triangles The Structure of Viruses: Helical and Icosahedral Shapes Figure 2.6 This is an icosahedron. Any idea how many sides an icosahedron has? 20 . An icosahedron is a geometric shape of 20 faces. Each face is an equilateral triangle. (A Dodecahedron has pentagons whereas an icosahedron has triangle faces.)

16. Icosahedral structure The Structure of Viruses: Helical and Icosahedral Shapes Figure 2.6 Parvovirus B19 Dengue virus Hepatitis B virus Norwalk virus

17. Icosahedral structure The Structure of Viruses: Helical and Icosahedral Shapes Figure 2.6 Vertex Edge Face

18. Icosahedral structure: Possesses ”2-3-5 Symmetry” 2-fold axis of symmetry (occurs when the axis is placed through the center of an edge. ) 3-fold axis of symmetry ( occurs when the axis is placed in the center of a face ) 5-fold axis of symmetry ( passes through a vertex of the icosahedron ) The Structure of Viruses: Helical and Icosahedral Shapes Figure 2.6 12 20 30 Number/ Icosahedron:

19. The Structure of Viruses: Helical 2-3-5 Symmetry

20. 1 subunit/face = 20 subunits total (not possible) 3 identical subunits/face = 60 subunits total 3 different subunits/face = 60 subunits total The Structure of Viruses: Helical and Icosahedral Shapes Icosahedral structure: Protein molecules are not triangular  several copies of a single viral protein, or several viral proteins, fit together to form the face of the icosahedron Its impossible to have 1 subunit per face

21. The Structure of Viruses: Helical and Icosahedral Shapes Icosahedral structure: Triangulation number (T) is the number of structural units per face of the icosahedron Virus capsids are composed of viral protein subunits that form structural units. The triangulation number (T) indicates the number of structural units per face of the icosahedron. In a T=1 virus, one structural unit (composed of 3 different protein subunits: gray , red, and blue) create the icosahedron face.

22. The Structure of Viruses: Helical and Icosahedral Shapes Icosahedral structure: Triangulation number (T) is the number of structural units per face of the icosahedron B Virion capsids with T=1, T=3, and T=4. The red lines outline a triangular face of the icosahedron, while the purple pentagons indicate the vertices (5-fold axes) of the icosahedron.

23. The Structure of Viruses: Helical and Icosahedral Shapes Icosahedral structure: Can be mathematically calculated by T=h 2 +hk+k 2 , where h and k are the number of structural units traversed in two different directions, respectively, to pass from one 5-fold axis to an adjacent 5-fold axis h k End here Start here k h T=h 2 +hk+k 2 h=1 k=1 T=1 2 +1(1)+1 2 T=1+1+1 T=3

24. The Structure of Viruses: Helical and Icosahedral Shapes Icosahedral structure: Can be mathematically calculated by T=h 2 +hk+k 2 , where h and k are the number of structural units traversed in two different directions, respectively, to pass from one 5-fold axis to an adjacent 5-fold axis h k End here Start here h T=h 2 +hk+k 2 h=2 k=0 T=2 2 +2(0)+0 2 T=4+0+0 T=4

25. Complex structure does not strictly conform to either helical or icosahedral structure. The Structure of Viruses: Complex Architecture Geminivirus Vaccinia virus Bacteriophage P2 Vaccinia virus (A), a virus belonging to the poxvirus family, has a complex capsid architecture with a dumbbell-shaped core. Geminiviruses (B) have a double-icosahedron capsid. Bacteriophages, such as P2 (C), often have complex capsid structure. Images courtesy of Ana Caceres et al. (A, PLoS Pathog . 2013; 9(11): e1003719), Kassie Kasdorf (B), and Mostafa Fatehi (C).

26. Classifying Viruses Taxonomy is assigning scientific names ( nomenclature ) to organisms. Not all viruses have yet been fully classified; some are in families but have not necessarily been placed in higher taxa, for example. International Committee on Taxonomy of Viruses https://talk.ictvonline.org/taxonomy/ Official taxonomic groups: Domain Kingdom Phylum Class Order Family Genus Species ----------- Realm ( عالم )

27. Classifying Viruses How does ICTV ( International Committee on Taxonomy of Viruses ) classify viruses? Virion properties (size, shape, envelope, capsid) Chemical and Physical properties Molecular weight Nucleotide sequence Number and types of different proteins Type of nucleic acid genome; replication strategy Host range Immune properties

28. Classifying Viruses Realm: - viria Kingdom: - virae Phylum: - viricota Class: - viricetes Order: - virales Family: - viridae Genus: - virus Species: may include common name Anything below species is the responsibility of the specific fields to create and catalog .

29. Classifying Viruses Realm: Riboviria Kingdom: Orthornavirae Phylum: Pisuviricota Class: Pisoniviricetes Order: Picornavirales Family: Picornaviridae Genus: Enterovirus Species: Enterovirus C Serotypes/Subtypes; Strains; Isolates; Variants; Mutants; Artificially-created laboratory strains

30. Classifying Viruses ICTV Guidelines: Latin binomial names are not used (e.g. Yersinia pestis). Virus names should not include any person’s name. When referring to the official taxonomy (order, families, subfamilies, genera, and species), the virus taxon should be written in italics with the first letter capitalized. Common usage or acronyms ( المختصرات ) are not italicized. Names should be meaningful.

31. “Some members of the Arenaviridae family can cause severe disease, including lymphocytic choriomeningitis virus and Lassa virus, which is named after the town in Nigeria where the first case occurred.”

32. Figure 2.11 Families of Viruses that Infect Vertebrates . Viruses are categorized based upon their type of nucleic acid (DNA viruses in yellow boxes and RNA viruses in purple boxes) and further classified based upon distinguishing characteristics. Note the nucleic acid, size, and architectural differences between viruses of different families. Viruses in color will be discussed in later chapters.

33. Following completion of this chapter, students should be able to: Explain the general properties of viruses; Reconstruct the architecture of helical and icosahedral viruses, identifying the components and viral proteins involved; Explain how viruses are classified and named. Learning Objectives