1. Bio 260
Viruses!!!

2. Viruses, and a half a second about viroids and prions
Chapter 13
Viruses, and a half a second about viroids and prions

3. Viral topics today Characteristics Structure Classification Culturing
Replication
Things that aren’t viruses

4. Some questions first How big is a virus? What is its structure?
How does it get into cells?
Can you tell viral relatedness based on symptoms?

5. How big?
5 um

6. General Characteristics of Viruses
Obligatory intracellular parasites
DNA or RNA
Protein coat
Some enclosed by envelope
Some have spikes
Most infect only specific types of cells in one host
Host range determined by specific host attachment sites and cellular factors

7. Virus Sizes
Figure 13.1

8. Filtration – will it remove viruses?
Membrane filtration removes microbes >0.22 µm
Other methods:
Autoclaving (steam heat)
Chemicals
Dry heat (longer time)
Figure 7.4

9. Virion Structure What’s a virus made of? Chemical composition?
Structural components?
Figure 13.2a

10. Virion Structure Nucleic acid DNA or RNA Capsid (protein) Capsomeres
Attachment proteins
spikes
Optional extras
Envelope (lipid)
Figure 13.2a

11. Virus – naked or enveloped
Naked viruses: outer coat is protein capsid made of capsomeres (subunits) (eg.phages and some animal)
WHY repeating subunits?
Enveloped viruses: lipid bilayer covers protein capsid (some animal)
WHERE did envelope come from?
Attachment proteins (spikes) either in capsid or envelope
WHAT determines host specificity?

12. Virus Morphologies polyhedral: composed of flat equilateral triangles
Icosahedral: 20 faces
Helical: filamentous or rod-like appearance
Enveloped: irregular shape
Complex: Isometric head and helical sheath or tail eg. phages

13. Morphology of a Polyhedral Virus
Nucleic acid (DNA or RNA)
Capsid (triangular faces)
made of capsomeres
Spikes (for what?)
Adenovirus –
common cold
Check the size

14. Morphology of a Helical Virus
What’s this
subunit?

15. Morphology of a Helical Virus
What’s this
subunit?

16. Morphology of an Enveloped Virus

17. Morphology of a Complex Virus
If you were to guess, which viruses would be the most complex?
Bacteriophages
Animal viruses
Plant viruses
Figure 13.5

18. Morphology of a Complex Virus
Figure 13.5

19. Viral Genome Usually very small, few genes
RNA or DNA, ss or ds (matters for replication and transcription)
What GENES will the virus need? (what proteins…)

20. Viral Genome Usually very small, few genes
RNA or DNA, ss or ds (matters for replication and transcription)
Genome must code for three things:
1) Viral protein coat
2) Replication of viral nucleic acids
3) Movement into and out of host cells

21. Genome structure matters
Genome structure: ss or ds DNA or RNA
Only (+) mRNA is translated into protein
Other genomes need to be transcribed to (+) mRNA
RNA replication unique to viruses; usually in cytoplasm
DNA replication usually in nucleus

22. Different strategies to achieve two goals
Make new genome (how??)
Make new capsid and other proteins (process??)

23. Different strategies to achieve two goals
Make new genome – DNA or RNA polymerase
Make new capsid and other proteins – transcription and translation aka expression
Viruses are all about genetics!
Terminology note: “viral replication” means all of the above (genome replication plus gene expression plus capsid assembly)

24. Preview of viral replication and gene expression

26. But don’t worry… we’ll talk more about that later. Meanwhile…
Characteristics
Structure
Classification
Culturing
Replication
Things that aren’t viruses

27. Classification of Viruses based on structure
Virus particle structure
Isometric, helical, pleomorphic, complex (bacteriophages)
Naked vs. enveloped
Genome structure
DNA or RNA; ss or ds; one molecule or segmented

28. Classification based on transmission
Enteric viruses: fecal-oral route  YAY!
(e.g., poliovirus, norovirus)
Respiratory viruses: inhaled droplets
(e.g., influenza virus, rhinovirus)
Sexually transmitted viruses
(e.g., herpes, papillomaviruses, HIV)
Zoonotic viruses: animal or arthropod vector
transmission can occur to humans or other animals
(e.g., rabies, West Nile virus, cowpox, dengue)

29. Growing Viruses - phage
Obligate intracellular parasite… meaning?
Viruses must be grown in living cells
Bacteriophages form plaques on a lawn of bacteria
START HJERE
Figure 13.6

30. Growing Viruses - animal
Animal viruses
may be grown in living animals OR
embryonated eggs
Figure 13.7

31. Growing Viruses - common
Animal and plant viruses can grow in cell culture
Continuous cell lines maintained indefinitely
Figure 13.8

32. Virus Identification Cytopathic effects Serological tests
DNA or RNA sequence

33. Virus Identification –cytopathic effect
Any detectable change after infection – range from shape change to death
Which is the infected side? A or B
Figure 13.9

34. Virus Identification –cytopathic effect
Any detectable change after infection – range from shape change to death
Uninfected – monolayer VSV infection: rounded
Figure 13.9

35. Serological tests Detect antibodies against viruses in a patient
Use antibodies to identify viruses in neutralization tests, viral hemagglutination, and Western blot

36. How do viruses replicate?

37. Virus life cycle in brief
Get in
Make more
Get out
Some variations on this theme
Figure 13.9

38. A Viral One-Step Growth Curve
Figure 13.10

39. Bacteriophage replication
DNA genomes
Lytic cycle
Lysogenic cycle

40. Lytic cycle Attachment and penetration get in
Biosynthesis and maturation make more
Lysis and release get out

41. The Lytic Cycle (bacteriophage)
Attachment: Phage attaches by tail fibers to host cell
Penetration: Phage lysozyme opens cell wall; tail sheath contracts to force tail core and DNA into cell
Biosynthesis: Production of phage DNA and proteins
Maturation: Assembly of phage particles
Release: Phage lysozyme breaks cell wall

42. Lytic Cycle of a T-Even Bacteriophage
attachment 1 2
penetration 3
biosynthesis
Figure 13.11

43. Lytic Cycle of a T-Even Bacteriophage
maturation 4
release
Figure 13.11

44. Viral infection of bacteria
Lytic cycle
Phage causes lysis and death of host cell
Lysogenic cycle
Prophage DNA incorporated in host DNA

45. The Lysogenic Cycle
“prophage” – when the phage DNA is in the host bacterial chromosome
Figure 13.12

46. The Lysogenic Cycle phage DNA incorporated in host DNA  ________
A form of horizontal gene transfer  ___________
Figure 13.12

47. The Lysogenic Cycle phage DNA incorporated in host DNA  Prophage
A form of horizontal gene transfer  Transduction
Figure 13.12

48. Why should we care about lysogeny (or transduction)
This exchange mediated by bacterial viruses is responsible for pathogenicity of many bacteria
Botulism toxin of C. botulinum originally from a virus
C. diphtheriae, also originally a viral (phage) source
Shiga toxin of E. coli, from Shigella
toxic shock syndrome of Streptococcus
I could go on…

49. Multiplication of Animal Viruses
Attachment: Viruses attach to cell membrane (spikes not tail fibers)
Penetration by endocytosis or fusion
Uncoating by viral or host enzymes
Biosynthesis: Production of nucleic acid and proteins
Maturation: Nucleic acid and capsid proteins assemble
Release by budding (enveloped viruses) or rupture

50. Getting in…
Animal virus options

51. If you’re naked… Attachment (how?) Penetration by endocytosis
Uncoating (what’s coming off?)
Figure 13.14a

52. Attachment, Penetration, Uncoating
By fusion (enveloped)
Figure 13.14b

53. A question about entry
Do both naked and enveloped viruses need to remove their coats?? A for yes, B for no

54. Getting OUT What do you think?
Animal virus 2 options – depend on structure
LYSIS
BUDDING

55. The dramatic way… lysis

56. Budding of an Enveloped Virus

57. How is viral structure related to entry/exit?
ENTER BY
EXIT BY
NAKED VIRUS
ENVELOPED VIRUS

58. How is viral structure related to entry/exit?
ENTER BY
EXIT BY
NAKED VIRUS
ENDOCYTOSIS  
LYSIS
ENVELOPED VIRUS
FUSION  
BUDDING

59. What happens in between
Biosynthesis, maturation – what’s the point?
Make new virus particles!!!

60. Multiplication of DNA Virus
release
uncoat
maturation
“early” proteins
(viral replication)
Get into nucleus
“late” proteins
(capsid)
Figure 13.15

61. If you’re a DNA virus What is copying your genome?
What’s making your mRNA?
DNA  DNA by host DNA polymerase
DNA m RNA by host RNA polymerase
mRNA  protein by host ribosomes

62. If you’re an RNA virus What is copying your genome?
What’s making your mRNA?
Are these obvious or simple questions to answer?

63. Some RNA virus terms Single stranded “+” RNA Single stranded “-” RNA
Double stranded RNA

64. Types of RNA genome

65. Multiplication of RNA-Containing Viruses
Only (+) mRNA is translated into protein
Other genomes need to be transcribed to (+) mRNA
Genome + mRNA  translate to protein and transcribe to –RNA
-RNA  + RNA for mRNA and genome
RNA to RNA HOW?
Viral RNA-dependent RNA polymerase (in the genome)
Figure 13.17

66. “+” stranded RNA genetics

67. Multiplication of RNA-Containing Viruses
Only (+) mRNA is translated into protein
Other genomes need to be transcribed to (+) mRNA
Genome - RNA  transcribe to +RNA
+RNA translate to protein, transcribe to –RNA genome
RNA to RNA HOW?
Viral RNA-dep RNA pol IN THE CAPSID
Figure 13.17

68. “-” stranded RNA genetics

69. Multiplication of RNA-Containing Viruses
Only (+) mRNA is translated into protein
Other genomes need to be transcribed to (+) mRNA
Genome dsRNA  use +RNA to make protein
RNA polymerase transcribes both strands to make new ds genome
RNA to RNA HOW?
RNA-dep RNA pol in the genome (+ side of ds RNA can be mRNA)
Figure 13.17

70. “ds” stranded RNA genetics

71. How is viral genome related to replication?
FUNCTION
REPLICATION requires
dsDNA
DNA polymerase
“+” RNA or dsRNA
Genome is an mRNA
Gene for RDRP (RNA dependent RNA pol)
“-” stranded RNA
RDRP protein loaded into the capsid

72. Anything ELSE???
Of COURSE there is. :D

73. Multiplication of a Retrovirus
HIV, leukemia, animal tumors
Single-stranded, enveloped, RNA viruses
reverse transcriptase: ss RNA  ds DNA
NO PROOFREADING, mistakes made, capsid proteins highly variable
ds DNA integrated into host chromosome = provirus
Figure 13.19

74. Multiplication of a Retrovirus
Entry by fusion
Release by budding
Uncoating releases
genome
enzymes
like RT,
integrase
Viral proteins to cell surface
RT ssDNAdsDNA
transcription 
viral genome
and proteins
Integration of provirus
Figure 13.19

75. Retrovirus replication

76. How animal viruses get mRNA and genomes
DNA viruses
DNA  DNA host DNA polymerase
sometimes also viral DNA polymerase
DNA mRNA host RNA polymerase
“+” RNA or ds RNA – their genome is already an mRNA
Genome is an mRNA used directly by ribosome
Encodes a Viral RNA RNA pol; makes more genomes
“-” RNA – their genome is NOT an mRNA
In capsid: viral RNA RNA pol makes mRNA
This RNA RNA polymerase also makes more genomes
Retroviruses – not “+” or “-” because of life cycle
In capsid: RNA DNA reverse transcriptase
Enters nucleus, incorporates into chromosome as provirus
Now treated as a gene so mRNA is made by host RNA pol

77. Cancer oncogenes Transformed cells how can you tell
transform normal cells into cancer cells
normal cell protein that is overactive or has extra functions due to mutation or misregulation
oncogenes are the result of mutation – radiation, chemicals, and 10% of the time gene transfer by viruses
Transformed cells how can you tell
Change shape: increased growth, loss of contact inhibition
Cell surface: tumor-specific transplant antigens
Genetic: oncogenic virus’ DNA integrated into host DNA

78. Do plants get viruses?
Yes!
Is their life cycle the same?
Figure 13.23

79. Plant Viruses -Very common
instead of attaching to receptors on cells enter through cell wall wounds
- Many extremely hardy
- Human, insect, worm, fungal vectors

80. Things that aren’t cells or viruses
But still cause disease
And they are REALLY REALLY small

81. Viroids are infectious RNAs in plants
It’s not PTSD, it’s PSTD: potato spindle tuber disease
Figure 13.23

82. Viroids Circular ssRNA ~300 to 400 nucleotides
Replicate autonomously within susceptible cells using host RNA polymerase
Single viroid capable of infecting cell
Resistant to digestion by nucleases
So far only host is plants
Sequences similar to introns
- Many questions: how do they replicate, how do they cause disease, how did they originate (“RNA world”), are they restricted to plants?

83. Prions Proteinaceous Infectious particle No nucleic acids!
Inherited and transmissible by ingestion, transplant, and surgical instruments
Spongiform encephalopathies: Sheep scrapie, Creutzfeldt-Jakob disease, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, mad cow disease
PrPC: Normal cellular prion protein, on cell surface
PrPSc: Scrapie protein; accumulates in brain cells, forming plaques

84. Sphongiform encephalopathies
PrPC: Normal cellular prion protein, on cell surface
PrPSc: Scrapie protein; accumulates in brain cells, forming plaques

85. How a Protein Can Be Infectious
Figure 13.22