Viruses

1. Viruses Chapter 6 Talaro

2. Viruses of bacteria, Archaea and eukaryotes

3. Smaller than bacteria Size of Viruses Pass through a filter Once called “filterable agents”

4. Taxonomy of Viruses • Originally based on disease • Now based mainly on three criterion • Nucleic acid type (DNA or RNA) • Strategy for replication • Morphology and size • Naming and classification decided on by International Committee on Taxonomy of Viruses (ICTV) • Order, Family, Subfamily, Genus, Species – Subspecies, strain etc. • Naming: -virales Order; -viridae, Family; -virinae Subfamily; -virus Genus, Species Epithet usually in English

5. Taxonomy of Viruses(Continued) • Ex. 1, Poliovirus Genus & Species: Enterovirus human poliovirus 1 Family: Picornaviridae Order: Not decided by ICTV • Ex. 2, Rabies Virus Genus & Species: Lyssavirus rabies virus Family: Rhabdoviridae Order: Mononegavirales

6. Species Concept in Virology • What is a virus “species”? After many years of controversy, in 1991, the ICTV accepted the definition of a virus species proposed by van Regenmortel (1990), as follows: "A virus species is defined as a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche." Members of a polythetic class are defined by more than one property and no single property is essential or necessary. One major advantage in this definition is that it can accommodate the inherent variability of viruses and it does not depend on the existence of a single unique characteristic.

7. Isolation, Cultivation, and Identification • Much more problematic than cultivation of organisms • Requires host cell for replication • Often times propagation of host cell is challenging • Mammalian tissue culture expensive and time • consuming

8. Viral Identification • Usually too small to see without electron microscopy • Nanometer range • Antibodies detect viral coat proteins • Western blot / ELISA technique to identify • (ELISA- Enzyme-Linked ImmunoSorbent Assay) • May also use tissue culture and observe characteristic • cytopathic effects • Newer methods use PCR to amplify virus specific DNA or • RNA sequences

9. Composition of Viruses -Viral genomes i. double-stranded DNA ii. single-stranded DNA iii. double-stranded RNA iv. single-stranded RNA - Nucleic acid can be organized as i. circular molecule ii. one or more linear molecules - Viruses range from simple (4 genes) to complex (100s of genes)

10. dsDNA (+) sense, template or transcribed strand (-) antisense or non-template stand (-) & (+) ssDNA dsRNA (+) ssRNA (for mRNA) (-) ssRNA (+) ssRNA (for DNA)

11. Capsids - Protein shell enclosing the genome - Built of large number of proteins called capsomeres - Capsid can be composed of 100s of sameor differentcapsomeres

12. Helical Shaped Viruses

13. Icosahedral Shaped Viruses • 20-sided with 12 corners • Vary in the number of capsomers • One edge is called a facet

14. Viral Envelopes - Not found in all viruses - Surrounds capsid - Derived from host cell (budding) - May have viral proteins and glycoproteins embedded - Assists the virus in infecting its host - Example is influenza

15. Viral Life Cycles Host Ranges - Viruses can only reproduce within a host cell - Viruses usually infect hosts by binding to receptors on the cell surface - Some viruses can infect many types of cells or many types of species (rabies for example) - Most viruses can only infect a few types of cells = limited host range - Eukaryotic viruses often attack specific tissues Cold virus = cells of upper respiratory track AIDS virus = T cells & macrophages of immune system Hepatitis = Only liver cells Polio = Intestinal & nerve cells Rabiesvirus = Nerve cells

16. No proof-reading enzymes so no repair Viral Mutation Rate • Mutation rate  1 in 10,000 nucleotides • (depends upon the virus) • Low-fidelity RNA polymerase (means not so accurate) • May recombine with different strains of the same virus • Reassortment of nucleic acid • Occasionally (rarely), acquire traits from completely • different virus • DNA & RNA viruses

17. Viral Replication Cycles Bacteriophage ldsDNA Influenza Virus (-) sensessRNA Human Immunodeficiency Virus (+) sense ssRNA for DNA

18. 6 Steps in Phage Replication • Adsorption – binding of virus to specific molecule on host cell • Penetration – viral genome enters host cell • Replication – viral components produced • Assembly - viral components assembled • Maturation – completion of viral formation • Release – viruses leave cell to infect other cells

19. Lytic Cycle Virulent Lysogenic Cycle Temperate Bacteria eater

20. l Fig 6.11

21. Viral genome has a promoter • Bacterial RNA polymerase transcribes viral genes • EARLY STAGE PROTEINS • Viral genes adjacent to the promoter are transcribed • Proteins that stop host transcription • Proteins that stimulate viral replication • Viral nucleases digest host genome • Stimulate late gene transcription • -LATE STAGE PROTEINS • Viral genes that code for viral capsid proteins • Proteins that lyse the host cell

22. Virus infects host Lytic Stage Host’s RNA polymerase transcribes EARLY genes operon Viral capsid proteins Early proteins stop transcription of host’s genes Early protein stimulates transcription of LATE genes. Early protein stimulates viral genome reproduction, digest host genome & stimulate late gene transcription Lyse host

23. Lysogenic Phage Cycle - Phage able to reproduce without destroying host - Temperate phages are able to use both the lytic and lysogenic cycles - When phage DNA enters cell, it uses site-specific recombination to insert its DNA into the host’s chromosome = prophage - The phage DNA is replicated and passed to daughter cells each time the bacteria divides - Occasionally, the prophage exits the bacterial DNA and engages in the lytic cycle - Exit from the lysogenic stage is often triggered by environmental cues/stresses

25. Temperate phage Bacterium growing well  lysogenic cycle Bacterial host stressed or damaged  lytic cycle cI Cro Regulatory proteins Compete for promoter sites Constant Growth Cro  cI  Lysogenic STRESS or UV Damage cI  Cro  Lytic

26. STRESS or DAMAGE Cro protein activates promoters for phage DNA replication & cell lysis GOOD GROWTH cI accumulates & activates promoters for integration Lysogenic Cycle

28. Animal Virus Adsorption Penetration Duplication/Synthesis Assembly Release

29. Adsorption • Glycoproteins on the envelope bind to • specific receptors on the host membrane • Cell receptor is also a glycoprotein • Envelopes fuse, viral capsid & • genome are transported inside cell • The receptors are involved in normal • cell functions • Rabies virus attaches to acetylcholine • receptor on nerve cells • HIV attaches to the CD4 receptor on T • and some other cells of the immune system

30. Penetration Endocytosis Fusion with cell membrane

31. Release by Budding or Exocytosis

32. Cytopathic Effects • Changes in size & shape • Cytoplasmic inclusion bodies • Nuclear inclusion bodies • Cells fuse to form multinucleated cells • Cell lysis • Alter DNA • Transform cells into cancerous cells (called Transformation but do not get confused with bacterial transformation) • Can see these effects microscopically in tissue culture cells infected with virus

33. Influenza (-) sense RNA virus Spanish Flu Epidemic 20 million deaths

34. (+) RNA = mRNA Negative Sense RNA Virus • An RNA virus whose genome is complementary to • mRNA • - Contains an RNA-dependent RNA polymerases • required for the synthesis of mRNA • Influenza virus • Genome consists of eight different negative sense • ss RNA strands • Strands 1 through 6 each encode one protein • - Strands 7 & 8 encode two proteins

35. Lipoprotein envelope Glycoprotein spikes Hemagglutinin Binds to a receptor found on eukaryotic respiratory mucosa cells RNA + nucleoprotein Matrix Nonspecific Neuraminidase Hydrolyzes the protective mucous coating, assists in viral budding, prevents virions from sticking together & helps in penetration Polymerase

36. Viral glycoproteins bind to host cell receptors Viral RNA is released Virus enters by endocytosis (-) (-) Viral RNA dependent RNA polymerase makes (+) RNA Viral RNA is translated • - Enveloped viruses do • not always kill host cell • Virus can be continuously • shed from infected cell • (factory) Virion assembled

37. Influenza viruses can infect humans, pigs, sea mammals • & birds • - Typically, one virus can only infect one type of host • Occasionally, some viral strains can infect another • animal host • Genome segments can be exchanged when two different • viral strains infect the same host • Some of the exchanged RNA segments encode for • glycoproteins • The virus can have glycoproteins from several hosts: • swine, human & bird • The same virus will appear as a “new” virus to • the human immune system because of different • glycoproteins

38. Each year, new strains of influenza emerge from southern China. The domestic duck is the main reservoir of influenza viruses in southern China. Geese are infrequently infected and chicken rarely. The domestic pig serves as the host for both avian and human influenza viruses. These viral strains recombine their genesto give rise to a novel influenza virus capable of human-to-human transmission. Reassortment Functional virions that contain combinations of of genomic segments from intracellular “pools” of viral strains

39. Influenza A viruses Infect humans, horses, pigs, ferrets and birds. A major human pathogen, that incites epidemics and pandemics. 15 known haemagglutinin (HA) serotypes and 9 known neuraminidase (NA) serotypes have been identified. Pigs and ducks are important reservoirs, that produce genetically/antigenically diverse viruses. The viruses are transferred back to humans via close contact between humans and animals. Influenza B viruses Only infects mammal and incite a mild form of influenza. Does not have distinguishable serotypes like influenza A. Influenza C viruses Only infects mammals, but it is unclear if they cause disease. Genetically and morphologically distinct from A and B types.

40. Novel Influenza A Strains Incite Pandemics 1918 Spanish flu 1957 Asian flu 1968 Hong Kong flu 1977 Russian flu Human Flu Transfers May Exceed Reports By DONALD G. McNEIL Jr. Published: June 4, 2006 The New York Times • Avian flu (H5N1) 1997 • - Type A virus • Easily transferred & highly virulent in chickens & wild birds • Not easily transferred to humans to date • - 105 human deaths in 186 confirmed cases (WHO Mar 24, 2006) • - Human deaths are associated with close exposure to infected chickens • H5N1 is not transmissible via aerosol droplets • Concern & debate regarding the no. of mutations required to • make this possible

41. How will H5N1 reach North America? Figure 2. Map of known routes for natural interhemispheric bird movement: route 1, migrants breeding in Alaska and wintering in East Asia; route 2, migrants breeding in East Asia and wintering along the Pacific Coast of North America; route 3, migrants breeding in Iceland or northwestern Europe and wintering along the Atlantic Coast of North America; route 4, vagrants from West Africa carried by tropical storm systems across the Atlantic to eastern North America. Birds and Influenza H5N1 Virus Movement to and within North America John H. Rappole* and Zdenek Hubálek†*Smithsonian Institution, Washington, DC, USA; and †Academy of Sciences, Valtice, Czech RepublicEmerging Infectious Diseases Vol. 12, No. 10 • October 2006

42. “The bird flu virus, known as A(H5N1), belongs to a group of influenza viruses known as Type A, which are the only ones that have caused pandemics. It has been steadily advancing around the world, first appearing in Asia, then Europe and Africa. The apparent lethality of A(H5N1), combined with its inexorable spread, are what have made scientists take it seriously. The virus lacks just one trait that could turn it into a pandemic: transmissibility, the ability to spread easily from person to person. If the virus acquires that ability, a worldwide epidemic could erupt. The A(H5N1) strains circulating now are quite different from the A(H5N1) strain detected in Hong Kong in 1997, which killed 6 of 18 human victims. Over time, A(H5N1) seems to have developed the ability to infect more and more species of birds, and has found its way into mammals -- specifically, cats that have eaten infected birds.” The New York Times Sunday, June 4, 2006

43. Aerosols– suspensions of fine dust and moisture in the air that contain pathogens