1. I. The Nature of Viruses 8.1 What Is a Virus?
8.2 Structure of the Virion
8.3 Overview of the Virus Life Cycle
8.4 Culturing, Detecting, and Counting Viruses

2. 8.1 What Is a Virus?
Virus: subcellular genetic element that cannot replicate independently of a living (host) cell
Virus particle (virion): extracellular form of a virus
Exists outside host and facilitates transmission from one host cell to another
Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material (Figure 8.1)

3. Viral genomes (Figure 8.2)
Either DNA or RNA genomes
Some are circular, but most are linear
Viruses
Genome:
DNA
RNA
RNA
DNA
Types:
ssDNA
dsDNA
ssRNA
dsRNA
ssRNA
(Retroviruses)
dsDNA
(Hepadnaviruses)
Single or double-stranded
Some have ability to reverse flow of information
Figure 8.2 Viral genomes.

4. 8.1 What Is a Virus? Virus taxonomy
Viruses are usually classified on the basis of the nucleic acid they contain
Particle shape and host range are less important

5. 8.2 Structure of the Virion
Viral structure
Genome: nucleic acid of the virus
Capsid: the protein shell that surrounds the genome of a virus particle (Figure 8.3)
Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
Capsid protein: individual protein molecule building block
Capsomere: visible subunit of the capsid
Smallest morphological unit visible with an electron microscope

6. 8.2 Structure of the Virion
Viral structure (cont'd)
Nucleocapsid: complete complex of nucleic acid and protein packaged in the virion
Enveloped virus: virus that contains additional layers around the nucleocapsid

7. Naked virus Enveloped virus (unenveloped) Figure 8.1 Nucleocapsid
Nucleic
acid
Nucleic
acid
Capsid
(composed of
capsid proteins)
Figure 8.1 Comparison of naked and enveloped virus particles.
Naked virus
(unenveloped)
Enveloped virus
Figure 8.1

8. 8.2 Structure of the Virion
Nucleocapsids are constructed in highly symmetric ways
Helical symmetry: rod-shaped viruses (e.g., tobacco mosaic virus)
Length of virus determined by length of nucleic acid
Width of virus determined by size and packaging of protein subunits
May or may not be surrounded by an envelope
Icosahedral symmetry: near-spherical viruses (e.g., human papillomavirus; Figure 8.4)
Most efficient arrangement of subunits in a closed shell

9. Figure 8.3 18 nm Structural subunits (capsomeres) Virus RNA
Figure 8.3 The arrangement of RNA and protein coat in a simple virus, tobacco mosaic virus.
Figure 8.3

10. Figure 8.4 5-Fold 3-Fold 2-Fold Cluster of 5 units “pentamer” Symmetry
Figure 8.4 Icosahedral symmetry.
Figure 8.4

11. Enveloped viruses (Figure 8.5)
Have membrane surrounding nucleocapsid (core)
Lipid bilayer with embedded proteins
Envelope makes initial contact with host cell
Figure 8.5 Enveloped viruses.
Figure 8.5

12. 8.2 Structure of the Virion
Some virions contain enzymes critical to infection
Lysozyme
Makes hole in cell wall
Lyses bacterial cell
Nucleic acid polymerases (reverse transcriptase)
Neuraminidases
Enzymes that cleave glycosidic bonds
Allows liberation of viruses from cell

13. 8.3 Overview of the Virus Life Cycle
Phases of viral replication (Figure 8.6)
Attachment (adsorption) of the virus to a susceptible host cell
Entry (penetration) of the virion or its nucleic acid
Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus
Assembly of capsids and packaging of viral genomes into new virions (maturation)
Release of mature virions from host cell

14. 8.3 Overview of the Virus Life Cycle (Bacteriophage)
Head
Protein coat
remains outside
Virions
Virion
DNA
Viral DNA enters
Cell (host) 1.
Attachment (adsorption of phage virion) 2.
Penetration
of viral
nucleic acid 3.
Synthesis of
viral nucleic acid
and protein 4.
Assembly and
packaging of
new viruses 5.
Cell lysis and
release of
new virions
Figure 8.6 The replication cycle of a bacterial virus.
Virus replication is typically characterized by a one-step growth curve (Figure 8.7)
Figure 8.6

15. Maturation Figure 8.7 Nucleic acid Protein coats Early enzymes Virus
Eclipse
Maturation
Early enzymes
Nucleic acid
Protein coats
Virus
added
Assembly and release
Figure 8.7 One-step growth curve of virus replication.
Latent period
Figure 8.7

16. 8.4 Culturing, Detecting, and Counting Viruses
Viruses replicate only in certain types of cells or in whole organisms
Bacterial viruses are easiest to grow; model systems
Animal viruses (and some plant viruses) can be cultivated in tissue or cell cultures
Plant viruses typically are most difficult because study often requires growth of whole plant

17. 8.4 Culturing, Detecting, and Counting Viruses
Plaques assay: are clear zones that develop on lawns of host cells
Bacterial lawn or tissue culture
Titer: number of infectious virus units detected per volume of fluid
Plaque assay: analogous to the bacterial colony; one way to measure virus infectivity (Figure 8.8)
Each plaque results from infection by a single virus particle

18. 1.
The cell–phage mixture
is poured onto a solidified
nutrient agar plate.
Mixture containing
molten top agar,
bacterial cells, and
diluted phage
suspension
Nutrient agar plate 2.
The mixture is left
to solidify.
Plaques
Sandwich of top agar and nutrient agar 3.
Incubation allows for
bacterial growth and
phage replication.
Phage plaques
Figure 8.8 Quantification of bacterial virus by plaque assay.
Lawn of host cells
Figure 8.8

19. Figure 8.9 Confluent monolayer of tissue culture cells Viral plaques
Figure 8.9 Animal cell cultures and viral plaques.
Confluent monolayer of tissue
culture cells
Viral plaques
Figure 8.9

20. II. Bacteriophage Life Cycles
8.5 Attachment and Entry of Bacteriophage T4
8.7 Replication of Bacteriophage T4
8.8 Temperate Bacteriophages and Lysogeny

21. 8.5 Attachment and Entry of Bacteriophage T4
Attachment of virion to host cell is highly specific
Requires complementary receptor molecules on the surface of a susceptible host and its infecting virus (Figure 8.10)
Receptors on host cell carry out normal functions for cell (e.g., uptake proteins, cell-to-cell interaction)
Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or complexes

22. Figure 8.10 Chi M13 T4 Flagellum Iron transport protein T1 Pilus ϕX174
MS2
LPS
Figure 8.10 Bacteriophage receptors.
Outer membrane
Peptidoglycan
Cytoplasmic membrane
Figure 8.10

23. 8.5 Attachment and Entry of Bacteriophage T4
The attachment of a virus to its host cell results in changes to both virus and cell surface that facilitate penetration
Permissive cell: host cell that allows the complete replication cycle of a virus to occur

24. 8.5 Attachment and Entry of Bacteriophage T4
Bacteriophage T4: virus of E. coli; one of the most complex penetration mechanisms (Figure 8.11)
Virions attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope
Tail fibers retract, and tail core makes contact with E. coli cell wall
Lysozyme-like enzyme forms small pore in peptidoglycan
Tail sheath contracts, and viral DNA passes into cytoplasm

25. Figure 8.11 T4 virion Tail fibers Tail pins Outer membrane Tail tube
Site of tail
lysozyme
activity
Peptidoglycan
Figure 8.11 Attachment of bacteriophage T4 to an Escherichia coli cell.
Cytoplasmic
membrane
Cytoplasm
T4 genome
Figure 8.11

26. 8. 7 Replication of Bacteriophage T4
T4 genome can be divided into three parts: early, middle, and late proteins (Figure 8.13)
Early and middle proteins: enzymes needed for DNA replication and transcription
Late proteins: head and tail proteins and enzymes required to liberate mature phage particles

27. Figure 8.13 Figure 8.13 Time course of events in phage T4 infection.
T4 nucleases,
DNA polymerase,
and new sigma factors
Phage T4 DNA
Phage head
proteins
Tail, collar, base plate, and tail fiber proteins
Mature T4 virion
T4 lysozyme
production
Infection
Phage DNA replication
Transcription
Early mRNA
Middle mRNA
Late mRNA
Self-assembly
Translation
Lysis
Figure 8.13 Time course of events in phage T4 infection.
Early proteins
Middle proteins
Late proteins 5 10 15 20 25
Minutes
Figure 8.13

28. 8. 7 Replication of Bacteriophage T4
Production of viral proteins
Early proteins (needed before replication
Enzyme for the synthesis and glucosylation of the T4 base hydroxymethylcytosine
Enzymes that function in T4 replisome
Proteins that modify host RNA polymerase
Middle proteins
Additional proteins that modify host RNA polymerase

29. 8. 7 Replication of Bacteriophage T4
Production of viral proteins (cont'd)
Late proteins (needed after replication)
Synthesized later
Include proteins of virus coat
Typically structural components
Synthesized in larger amounts

30. 8. 7 Replication of Bacteriophage T4
Stepwise Packaging the T4 genome (Figure 8.14)
Precursor of bacteriophage head is assembled
Packaging motor is assembled
Double-stranded DNA is pumped into head under pressure using ATP
After head is filled with DNA, T4 tail, tail fibers, and other components are added

31. Figure 8.14 Figure 8.14 Packaging of DNA into a T4 phage head. ATP
Prohead
Motor
Packaging
motor
complex
Mature virion
ATP
Scaffold proteins
Packaging motor attaches to
prohead.
Scaffold
proteins discarded
Other
assembly
steps
Packaging
motor
discarded
Capsid proteins
dsDNA
Portal proteins
Figure 8.14 Packaging of DNA into a T4 phage head.
Figure 8.14

32. 8.8 Temperate Bacteriophages and Lysogeny
Viral life cycles
Virulent mode: viruses lyse host cells after infection-T4 is an example (aka lytic pathway or cycle)
Temperate mode: viruses replicate their genomes in tandem with host genome and without killing host-phage lambda is an example (aka lysogenic pathway or cycle)

33. 8.8 Temperate Bacteriophages and Lysogeny
Temperate viruses: can undergo a stable genetic relationship within the host (Figure 8.15)
Lysogeny: state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
Lysogen: a bacterium containing a prophage
Under certain conditions, lysogenic viruses may revert to the lytic pathway and begin to produce virions

34. Temperate virus
Host DNA
Viral DNA
Attachment of the virus to the host cell
Cell (host)
Injection of viral DNA
Lytic pathway
Lysogenic pathway
Lytic events are initiated.
Induction
Phage components are synthesized and virions are assembled.
Viral DNA is integrated
into host DNA.
Lysogenized
cell
Figure 8.15 Consequences of infection by a temperate bacteriophage.
Prophage
Lysis of the host cell and release of new phage virions
Viral DNA is replicated with host DNA at cell division.
Figure 8.15

35. 8.8 Temperate Bacteriophages and Lysogeny
Lambda DNA forms a circle
Attaches to host DNA and integrates itself into DNA
Lambda “att” site
Lambda repressor protein keeps lambda genes shut off
Unfavorable cell growth conditions tend to favor lysogenic pathway
Lysogeny stable until cell is injured or damaged

36. 8.8 Temperate Bacteriophages and Lysogeny
Unusual mode of replication for lambda DNA When it enters lytic pathway, lambda synthesizes long, linear concatemers of DNA by rolling circle replication (Figure 8.17b) Not standard replication fork as used for host DNA

37. Figure 8.17b 3′ RNA primers Roll One lambda genome
Figure 8.17b Integration of lambda DNA and rolling circle replication.
Rolling circle replication of lambda genome
Figure 8.17b

38. III. Viral Diversity and Ecology
8.9 An Overview of Bacterial Viruses
8.10 An Overview of Animal Viruses
8.11 The Virosphere and Viral Ecology

39. 8.9 An Overview of Bacterial Viruses
Bacteriophages are very diverse (Figure 8.19)
Best-studied bacteriophages infect enteric bacteria
Examples of hosts: E. coli, Salmonella enterica
Most phages contain dsDNA genomes
Most are naked, but some possess lipid envelopes
They are structurally complex, containing heads, tails, and other components (Figure 8.20)

40. Figure 8.19 Schematic representations of the main types of bacterial viruses.

41. 8.10 An Overview of Animal Viruses
Often, entire virion enters the animal cell, unlike in prokaryotes
Nucleus is the site of replication for many animal viruses
Animal viruses contain all known modes of viral genome replication (Figure 8.21)
There are many more kinds of enveloped animal viruses than enveloped bacterial viruses
As animal viruses leave host cell, they can remove part of host cell's lipid bilayer for their envelope

42. Figure 8.21 Diversity of animal viruses.

43. 8.10 An Overview of Animal Viruses
Consequences of virus infection in animal cells (Figure 8.22)
Persistent infections: release of virions from host cell does not result in cell lysis
Infected cell remains alive and continues to produce virus
Latent infections: delay between infection by the virus and lytic events
Transformation: conversion of normal cell into tumor cell

44. Figure 8.22 Formation of proviral state and transformation
into tumor cell
Transformation
Tumor cell
division
Cell
Virus
Death of the cell and release of the virus
Lysis
Virus
multiplication
Slow release of
virus without
causing cell death
Persistent
infection
Figure 8.22 Possible effects that animal viruses may have on cells they infect.
Virus present
but not
replicating
May revert to
lytic infection
Latent
infection
Figure 8.22

45. 8.10 An Overview of Animal Viruses
Retroviruses: RNA viruses that replicate through a DNA intermediate
Enveloped viruses (Figure 8.23a)
Contain a reverse transcriptase (copies information from its RNA genome into DNA), integrase, and protease
DNA copy is called a cDNA
Integrates into host DNA

46. Integrated retrovirus cDNA is called a provirus
1. Entry and uncoating
of the retrovirus
ssRNA
(viral genome)
2. Reverse transcriptase
activity (two steps)
Integrated
retrovirus
cDNA is
called a
provirus
dsDNA
3. Viral DNA enters nucleus and
integrates into the host genome.
Host DNA
Viral DNA
4. Transcription by host RNA
polymerase forms viral mRNA
and genome copies.
ssRNA
5. Translation of mRNA forms viral
proteins; new nucleocapsids
assembled and released by budding.
Figure 8.24 Replication of a retrovirus.
Host cytoplasmic
membrane

47. 8.11 The Virosphere and Viral Ecology
About 106 prokaryotes per ml of seawater (Figure 8.25)
About 107 viruses per ml of seawater
Bacteriophages thought to have major impact on evolution of Bacteria
May confer new metabolic or other beneficial properties
Many of the prokaryotes in seawater are Archaea
Many of the viruses in seawater may infect marine Archaea

48. 8.11 The Virosphere and Viral Ecology
Most of Earth's genetic diversity resides in viruses
Most viruses are believed to be bacteriophages
Viral metagenome: the sum total of all viral genes in a particular environment
Most viruses are undiscovered
Most viral genes have unknown function