1. 17
Viruses

2. Overview: A Borrowed Life
A virus is an infectious particle consisting of little more than genes packaged into a protein coat
Viruses lead “a kind of borrowed life,” existing in a shady area between life-forms and chemicals 2

3. Figure 17.1
Figure 17.1 Are the tiny viruses (red) budding from this cell alive?
0.25 m 3

4. Concept 17.1: A virus consists of a nucleic acid surrounded by a protein coat
Even the largest known virus is barely visible under the light microscope
Some viruses can be crystalized
Viruses are not cells but are a nucleic acid enclosed in a protein coat

5. Viral Genomes Viral genomes may consist of either
Double- or single-stranded DNA, or
Double- or single-stranded RNA
Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus 5

6. Capsids and Envelopes
A capsid is the protein shell that encloses the viral genome
Capsids are built from protein subunits called capsomeres
A capsid can have various structures 6

7. (a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses
Figure 17.2
Membranous
envelope
Capsomere
RNA
RNA
DNA
Capsid
Head
DNA
Capsomere of capsid
Tail sheath
Tail fiber
Glycoprotein
Glycoproteins
18  250 nm
70–90 nm (diameter)
80–200 nm (diameter)
80  225 nm
Figure 17.2 Viral structure
20 nm
50 nm
50 nm
50 nm
(a) Tobacco mosaic virus
(b) Adenoviruses
(c) Influenza viruses
(d) Bacteriophage T4 7

8. (a) Tobacco mosaic virus (b) Adenoviruses
Figure 17.2a
RNA
Capsomere
DNA
Capsomere of capsid
Glycoprotein
18  250 nm
70–90 nm (diameter)
Figure 17.2a Viral structure (part 1: TMV and adenovirus)
20 nm
50 nm
(a) Tobacco mosaic virus
(b) Adenoviruses 8

9. (a) Tobacco mosaic virus
Figure 17.2aa
Figure 17.2aa Viral structure (part 1a: TMV)
20 nm
(a) Tobacco mosaic virus 9

10. 50 nm (b) Adenoviruses Figure 17.2ab
Figure 17.2ab Viral structure (part 1b: adenovirus)
50 nm
(b) Adenoviruses 10

11. Membranous envelope RNA Head Capsid DNA Tail sheath Tail fiber
Figure 17.2b
Membranous
envelope
RNA
Head
Capsid
DNA
Tail sheath
Tail fiber
Glycoproteins
80–200 nm (diameter)
80  225 nm
Figure 17.2b Viral structure (part 2: influenza and bacteriophage T4)
50 nm
50 nm
(c) Influenza viruses
(d) Bacteriophage T4 11

12. 50 nm (c) Influenza viruses Figure 17.2ba
Figure 17.2ba Viral structure (part 2a: influenza)
50 nm
(c) Influenza viruses 12

13. 50 nm (d) Bacteriophage T4 Figure 17.2bb
Figure 17.2bb Viral structure (part 2b: bacteriophage T4)
50 nm
(d) Bacteriophage T4 13

14. Some viruses have membranous envelopes that help them infect hosts
These viral envelopes are derived from the host cell’s membrane and contain a combination of viral and host cell molecules 14

15. Bacteriophages, also called phages, are viruses that infect bacteria
They have the most complex capsids found among viruses
Phages have an elongated capsid head that encloses their DNA
A protein tail piece attaches the phage to the host and injects the phage DNA inside 15

16. Concept 17.2: Viruses replicate only in host cells
Viruses are obligate intracellular parasites, which means they can replicate only within a host cell
Each virus has a host range, a limited number of host cells that it can infect 16

17. General Features of Viral Replicative Cycles
Once a viral genome has entered a cell, the cell begins to manufacture viral proteins
The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules
Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses
These exit from the host cell, usually damaging or destroying it
Animation: Simplified Viral Replicative Cycle 17

18. Transcription and manufacture of capsid proteins
Figure 17.3
VIRUS
DNA 1
Entry and uncoating 3
Transcription and manufacture of capsid proteins
Capsid 2
Replication
HOST CELL
Viral DNA
mRNA
Capsid proteins
Viral DNA
Figure 17.3 A simplified viral replicative cycle 4
Self-assembly of new virus particles and their exit from the cell 18

19. Replicative Cycles of Phages
Phages are the best understood of all viruses
Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle 19

20. The Lytic Cycle
The lytic cycle is a phage replicative cycle that culminates in the death of the host cell
The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the progeny viruses
A phage that reproduces only by the lytic cycle is called a virulent phage
Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA
Animation: Phage T4 Lytic Cycle 20

21. Figure 1
Attachment
Figure The lytic cycle of phage T4, a virulent phage (step 1) 21

22. Entry of phage DNA and degradation of host DNA
Figure 1
Attachment 2
Entry of phage DNA and degradation of host DNA
Figure The lytic cycle of phage T4, a virulent phage (step 2) 22

23. Entry of phage DNA and degradation of host DNA
Figure 1
Attachment 2
Entry of phage DNA and degradation of host DNA
Figure The lytic cycle of phage T4, a virulent phage (step 3) 3
Synthesis of viral genomes and proteins 23

24. Entry of phage DNA and degradation of host DNA
Figure 1
Attachment 2
Entry of phage DNA and degradation of host DNA
Phage assembly
Figure The lytic cycle of phage T4, a virulent phage (step 4) 4
Assembly 3
Synthesis of viral genomes and proteins
Head
Tail
Tail fibers 24

25. Entry of phage DNA and degradation of host DNA
Figure 1
Attachment 2
Entry of phage DNA and degradation of host DNA 5
Release
Phage assembly
Figure The lytic cycle of phage T4, a virulent phage (step 5) 4
Assembly 3
Synthesis of viral genomes and proteins
Head
Tail
Tail fibers 25

26. The Lysogenic Cycle
The lysogenic cycle replicates the phage genome without destroying the host
Phages that use both the lytic and lysogenic cycles are called temperate phages
The viral DNA molecule is incorporated into the host cell’s chromosome
This integrated viral DNA is known as a prophage 26

27. Every time the host divides, it copies the phage DNA and passes the copies to daughter cells
A single infected cell can give rise to a large population of bacteria carrying the virus in prophage form
An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode
Animation: Phage  Lysogenic and Lytic Cycles

28. Daughter cell with prophage Phage DNA The phage injects its DNA.
Figure 17.5
Daughter cell with prophage
Phage DNA
The phage injects its DNA.
Many cell divisions create many infected bacteria.
Phage DNA circularizes.
Phage
Bacterial chromosome
Prophage exits chromosome.
Lytic cycle
Lysogenic cycle
Prophage is copied with bacterial chromosome.
The cell lyses, releasing phages.
Figure 17.5 The lytic and lysogenic cycles of phage λ, a temperate phage
Prophage
Phage DNA and proteins are synthesized and assembled.
Phage DNA integrates into bacterial chromosome. 28

29. The phage injects its DNA.
Figure 17.5a
Phage DNA
The phage injects its DNA.
Phage DNA circularizes.
Phage
Bacterial chromosome
Lytic cycle
The cell lyses, releasing phages.
Figure 17.5a The lytic and lysogenic cycles of phage λ, a temperate phage (part 1: lytic)
Phage DNA and proteins are synthesized and assembled. 29

30. Daughter cell with prophage
Figure 17.5b
Daughter cell with prophage
Many cell divisions create many infected bacteria.
Prophage exits chromosome.
Lysogenic cycle
Prophage is copied with bacterial chromosome.
Figure 17.5b The lytic and lysogenic cycles of phage λ, a temperate phage (part 2: lysogenic)
Prophage
Phage DNA integrates into bacterial chromosome. 30

31. Replicative Cycles of Animal Viruses
There are two key variables used to classify viruses that infect animals
The nature of the viral genome (single- or double- stranded DNA or RNA)
The presence or absence of an envelope 31

32. Viral Envelopes
An animal virus with an envelope uses it to enter the host cell
The envelope is derived from the plasma membrane of a host cell, although some of the molecules on the envelope are specified by the genome of the virus 32

33. Envelope (with glycoproteins) Viral genome (RNA) Template
Figure 17.6
Capsid
RNA
HOST CELL
Envelope (with glycoproteins)
Viral genome (RNA)
Template
mRNA
Capsid proteins ER
Copy of genome
(RNA)
Figure 17.6 The replicative cycle of an enveloped RNA virus
Glycoproteins
New virus 33

34. RNA as Viral Genetic Material
The broadest variety of RNA genomes is found in viruses that infect animals
Retroviruses use reverse transcriptase to copy their RNA genome into DNA
HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome) 34

35. Viral DNA that is integrated into the host genome is called a provirus
Unlike a prophage, a provirus is a permanent resident of the host cell
The host’s RNA polymerase transcribes the proviral DNA into RNA molecules
The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new viruses released from the cell
Animation: HIV Replicative Cycle 35

36. HIV Membrane of white blood cell Viral envelope Glycoprotein HIV
Figure 17.7
Membrane of white blood cell
Viral envelope
Glycoprotein
HIV
Capsid
RNA (two identical strands)
HOST CELL
HIV
Reverse transcriptase
Reverse transcriptase
Viral RNA
RNA-DNA hybrid
0.25 m
DNA
HIV entering a cell
NUCLEUS
Provirus
Chromosomal DNA
RNA genome for the next viral generation
Figure 17.7 The replicative cycle of HIV, the retrovirus that causes AIDS
mRNA
New virus
New HIV leaving a cell 36

37. HIV Viral envelope Glycoprotein Capsid RNA (two identical strands)
Figure 17.7a
Viral envelope
Glycoprotein
Capsid
RNA (two identical strands)
HOST CELL
HIV
Reverse transcriptase
Reverse transcriptase
Viral RNA
RNA-DNA hybrid
DNA
NUCLEUS
Provirus
Chromosomal DNA
RNA genome for the next viral generation
Figure 17.7a The replicative cycle of HIV, the retrovirus that causes AIDS (part 1: detail)
mRNA
New virus 37

38. RNA (two identical strands)
Figure 17.7aa
Viral envelope
Glycoprotein
Capsid
RNA (two identical strands)
HOST CELL
HIV
Reverse transcriptase
Reverse transcriptase
Viral RNA
RNA-DNA hybrid
Figure 17.7aa The replicative cycle of HIV, the retrovirus that causes AIDS (part 1a: detail of entry)
DNA 38

39. RNA genome for the next viral generation
Figure 17.7ab
NUCLEUS
Provirus
Chromosomal DNA
RNA genome for the next viral generation
mRNA
Figure 17.7ab The replicative cycle of HIV, the retrovirus that causes AIDS (part 1b: detail of release)
New virus 39

40. Membrane of white blood cell
Figure 17.7b
Membrane of white blood cell
HIV
Figure 17.7b The replicative cycle of HIV, the retrovirus that causes AIDS (part 2: TEMs)
0.25 m
HIV entering a cell
New HIV leaving a cell 40

41. Membrane of white blood cell
Figure 17.7ba
Membrane of white blood cell
HIV
Figure 17.7ba The replicative cycle of HIV, the retrovirus that causes AIDS (part 2a: HIV entry, TEM)
0.25 m
HIV entering a cell 41

42. 0.25 m HIV entering a cell Figure 17.7bb
Figure 17.7bb The replicative cycle of HIV, the retrovirus that causes AIDS (part 2b: HIV entry, TEM)
HIV entering a cell 42

43. 0.25 m New HIV leaving a cell Figure 17.7bc
Figure 17.7bc The replicative cycle of HIV, the retrovirus that causes AIDS (part 2c: HIV release, TEM)
New HIV leaving a cell 43

44. 0.25 m New HIV leaving a cell Figure 17.7bd
Figure 17.7bd The replicative cycle of HIV, the retrovirus that causes AIDS (part 2d: HIV release, TEM)
New HIV leaving a cell 44

45. 0.25 m New HIV leaving a cell Figure 17.7be
Figure 17.7be The replicative cycle of HIV, the retrovirus that causes AIDS (part 2e: HIV release, TEM)
New HIV leaving a cell 45

46. Evolution of Viruses
Viruses do not fit our definition of living organisms
Since viruses can replicate only within cells, they probably evolved after the first cells appeared
Candidates for the source of viral genomes are plasmids (circular DNA in bacteria and yeasts) and transposons (small mobile DNA segments)
Plasmids, transposons, and viruses are all mobile genetic elements 46

47. Concept 17.3: Viruses are formidable pathogens in animals and plants
Diseases caused by viral infections afflict humans, agricultural crops, and livestock worldwide 47

48. Viral Diseases in Animals
Viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes
Some viruses cause infected cells to produce toxins that lead to disease symptoms
Others have molecular components such as envelope proteins that are toxic 48

49. Vaccines can prevent certain viral illnesses
A vaccine is a harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
Vaccines can prevent certain viral illnesses
Viral infections cannot be treated by antibiotics
Antiviral drugs can help to treat, though not cure, viral infections 49

50. Emerging Viruses
Viruses that suddenly become apparent are called emerging viruses
HIV is a classic example
The West Nile virus appeared in North America first in 1999 and has now spread to all 48 contiguous states 50

51. In 2009 a general outbreak, or epidemic, of a flu-like illness occurred in Mexico and the United States; the virus responsible was named H1N1
H1N1 spread rapidly, causing a pandemic, or global epidemic

52. 1 m (a) 2009 pandemic H1N1 influenza A virus
Figure 17.8
Figure 17.8 Influenza in humans
1 m
(a) 2009 pandemic H1N1 influenza A virus
(b) 2009 pandemic screening 52

53. 1 m (a) 2009 pandemic H1N1 influenza A virus Figure 17.8a
Figure 17.8a Influenza in humans (part 1: SEM)
1 m
(a) 2009 pandemic H1N1 influenza A virus 53

54. (b) 2009 pandemic screening
Figure 17.8b
Figure 17.8b Influenza in humans (part 2: screening)
(b) 2009 pandemic screening 54

55. Three processes contribute to the emergence of viral diseases
The mutation of existing viruses, which is especially high in RNA viruses
Dissemination of a viral disease from a small, isolated human population, allowing the disease to go unnoticed before it begins to spread
Spread of existing viruses from animal populations; about three-quarters of new human diseases originate this way

56. Strains of influenza A are given standardized names
The name H1N1 identifies forms of two viral surface proteins, hemagglutinin (H) and neuraminidase (N)
There are numerous types of hemagglutinin and neuraminidase, identified by numbers

57. Viral Diseases in Plants
More than 2,000 types of viral diseases of plants are known; these have enormous impacts on the agricultural and horticultural industries
Plant viruses have the same basic structure and mode of replication as animal viruses
Most plant viruses known thus far have an RNA genome and many have a helical capsid 57

58. Plant viral diseases spread by two major routes
Infection from an external source of virus is called horizontal transmission
Herbivores, especially insects, pose a double threat because they can both carry a virus and help it get past the plant’s outer layer of cells
Inheritance of the virus from a parent is called vertical transmission 58

59. Figure 17.UN01
Figure 17.UN01 In-text figure, infected squash, p. 341 59

60. Figure 17.UN02a
A/California/07/2009
Group 1
A/Taiwan/1164/2010
Group 3
A/Taiwan/T1773/2009
Group 6
A/Taiwan/T1338/2009
A/Taiwan/T0724/2009
A/Taiwan/T1821/2009
A/Taiwan/937/2009
A/Taiwan/T1339/2009
Group 7
A/Taiwan/940/2009
A/Taiwan/7418/2009
A/Taiwan/8575/2009
A/Taiwan/4909/2009
A/Taiwan/8542/2009
A/Taiwan/1018/2011
Group 9
A/Taiwan/552/2011
A/Taiwan/2826/2009
A/Taiwan/T0826/2009
A/Taiwan/1017/2009
A/Taiwan/7873/2009
A/Taiwan/11706/2009
Group 8
A/Taiwan/6078/2009
A/Taiwan/6341/2009
A/Taiwan/6200/2009
Figure 17.UN02a Skills exercise: analyzing a DNA sequence-based phylogenetic tree to understand viral evolution (part 1)
A/Taiwan/5270/2010
Group 8-1
A/Taiwan/3994/2010
A/Taiwan/2649/2011
Group 10
A/Taiwan/1102/2011
A/Taiwan/4501/2011
A/Taiwan/67/2011
A/Taiwan/1749/2011
A/Taiwan/4611/2011
A/Taiwan/5506/2011
Group 11
A/Taiwan/1150/2011
A/Taiwan/2883/2011
A/Taiwan/842/2010
A/Taiwan/3697/2011 60

61. A/California/07/2009 Group 1 A/Taiwan/1164/2010 Group 3
Figure 17.UN02aa
A/California/07/2009
Group 1
A/Taiwan/1164/2010
Group 3
A/Taiwan/T1773/2009
Group 6
A/Taiwan/T1338/2009
A/Taiwan/T0724/2009
A/Taiwan/T1821/2009
A/Taiwan/937/2009
A/Taiwan/T1339/2009
Group 7
A/Taiwan/940/2009
A/Taiwan/7418/2009
A/Taiwan/8575/2009
A/Taiwan/4909/2009
A/Taiwan/8542/2009
Figure 17.UN02aa Skills exercise: analyzing a DNA sequence-based phylogenetic tree to understand viral evolution (part 1a)
A/Taiwan/1018/2011
Group 9
A/Taiwan/552/2011
A/Taiwan/2826/2009
A/Taiwan/T0826/2009 61

62. A/Taiwan/1017/2009 A/Taiwan/7873/2009 A/Taiwan/11706/2009 Group 8
Figure 17.UN02ab
A/Taiwan/1017/2009
A/Taiwan/7873/2009
A/Taiwan/11706/2009
Group 8
A/Taiwan/6078/2009
A/Taiwan/6341/2009
A/Taiwan/6200/2009
A/Taiwan/5270/2010
Group 8-1
A/Taiwan/3994/2010
A/Taiwan/2649/2011
Group 10
A/Taiwan/1102/2011
A/Taiwan/4501/2011
A/Taiwan/67/2011
A/Taiwan/1749/2011
A/Taiwan/4611/2011
Figure 17.UN02ab Skills exercise: analyzing a DNA sequence-based phylogenetic tree to understand viral evolution (part 1b)
A/Taiwan/5506/2011
Group 11
A/Taiwan/1150/2011
A/Taiwan/2883/2011
A/Taiwan/842/2010
A/Taiwan/3697/2011 62

63. Number of viral isolates
Figure 17.UN02b
Wave 1
Wave 2
Interwave
Wave 3
800
700
Key
600
Groups 1, 3, 6
Number of viral isolates
500
Group 7
Group 8
400
Group 8-1
300
Group 9
Group 10
200
Group 11
100
Figure 17.UN02b Skills exercise: analyzing a DNA sequence-based phylogenetic tree to understand viral evolution (part 2) M J J A S O N D J F M A M J J A S O N D J F M A
2009
2010
2011 63

64. The phage attaches to a host cell and injects its DNA. Phage DNA
Figure 17.UN03
The phage attaches to a host cell and injects its DNA.
Phage DNA
Bacterial chromosome
Prophage
Lytic cycle
Lysogenic cycle
• Virulent or temperate phage • Destruction of host DNA • Production of new phages • Lysis of host cell causes release of progeny phages
• Temperate phage only • Genome integrates into bacterial chromosome as prophage, which (1) is replicated and passed on to daughter cells and (2) can be induced to leave the chromosome and initiate a lytic cycle
Figure 17.UN03 Summary of key concepts: lytic and lysogenic cycles 64

65. Number of bacteria Number of viruses A B Time Time Figure 17.UN04
Figure 17.UN04 Test your understanding, question 7 (growth curves)
Time
Time 65