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Virology - Principles and Applications$ s8 A4 T9 |) F+ F' L3 ^9 r
Dr John Carter (Liverpool John Moores University, UK), Prof Venetia Saunders (Liverpool John Moores University, UK)
August 2007, ©2007
by Dr John Carter, Prof Venetia Saunders! X7 J; T  z3 k* |; d% j! {
ISBN 978-0-470-02387-7; O. S1 s, v8 j( V0 s! g
Preface.- w, X( [& n4 A. s1 U

Abbreviations used in this book.* J) r% E( n& ]5 Z! O: D* v( s

Greek letters used in this book.( i+ }! r2 j2 m8 T9 a9 h7 M# D

Colour coding for molecules.
& o$ S% T- n5 I5 k6 [
1 Viruses and their importance.% Z0 W: |' w* \7 x1 M

1.1 Viruses are ubiquitous on Earth.1 z4 h7 C+ E( |5 m& w2 p3 T
" w. _6 K9 c3 u) d# ]- f6 [
1.2 Reasons for studying viruses.

1.3 The nature of viruses.
* z* p6 k! F: E
1.4 The remainder of the book.* T, L0 S. A- o
- ~* ~+ [! w9 v7 h
2 Methods used in virology.- d- P. a# o+ z8 _, H1 @' y

2.1 Introduction to methods used in virology.
0 K+ l9 A3 H% m2 T; a" d; R0 y, a# Y
2.2 Cultivation of viruses.
  v0 D4 C; A$ @$ i
2.3 Isolation of viruses." `; {8 B1 {, [- @( Q8 v
. A# j: h" }2 i4 {  P8 r* c- m$ I
2.4 Centrifugation.

2.5 Structural investigations of cells and virions./ Q) U4 H0 _6 A6 I

2.6 Electrophoretic techniques.

2.7 Detection of viruses and virus components.

2.8 Infectivity assays.

2.9 Virus genetics.5 A8 n! h$ U4 M' ~

3 Virus structure.

3.1 Introduction to virus structure.$ |4 V3 R2 o7 A6 i" {: w1 t
9 Z$ W7 g9 o4 ^% v) Q0 W
3.2 Virus genomes.
6 P) i4 C7 \+ u. V) }0 p
3.3 Virus proteins.5 t2 h, z9 i# s, r/ S& h, D

3.4 Capsids.; Z9 D' u  _4 k6 ~4 p4 F

3.5 Virion membranes.- ~0 ^( c$ g/ U! ^' b7 K

3.6 Occlusion bodies.4 ^; O0 h+ b) k* a4 E
: n& g* o& v+ ?5 |% K' M* {
3.7 Other virion components.. J% X2 w# S0 q, }% ^

4 Virus transmission.

4.1 Introduction to virus transmission.
5 S8 `! F3 m) Z( M8 M/ \: z
4.2 Transmission of plant viruses.

4.3 Transmission of vertebrate viruses.5 H5 e5 w& V& B

4.4 Transmission of invertebrate viruses.3 n6 D1 a1 u1 g' H3 r: E' d
. f( q; n( C; ~5 x
4.5 Permissive cells.; P" m- ?. W7 U' W" X) A5 }

5 Attachment and entry of viruses into cells.
/ T9 ]; _5 Z& O& c# y. }9 b
5.1 Overview of virus replication.

5.2 Animal viruses.; y! s+ N4 d9 s; N
, J+ i1 [3 s8 L1 y  S5 {5 n- S
5.3 Bacteriophages.; z  T% s0 q6 S  [  Q5 k0 c" O
# ~2 c: }2 O, r/ G& g
6 Transcription, translation and transport.$ b) \, Y7 Q% _8 _

6.1 Introduction to transcription, translation and transport.: {  ]" J9 ?4 s( ?) y

6.2 Transcription of virus genomes./ r  R* ^9 q' r4 R

6.3 Transcription in eukaryotes.
$ D, i4 y" ]8 r7 K  [
6.4 Translation in eukaryotes.2 u) L$ `! T& Z6 V6 L) Y

6.5 Transport in eukaryotic cells.

6.6 Transcription and translation in bacteria.4 \) O! l) A; m8 a( A& s! j

7 Virus genome replication.1 f& ]6 b. V9 R1 R! [- C$ K% S& D

7.1 Overview of virus genome replication.

7.2 Locations of virus genome replication in eukaryotic cells.

7.3 Initiation of genome replication.
. x! M! z+ D! Z: v
7.4 Polymerases.
, @$ }0 Y! W( j8 f# Z+ r
7.5 DNA replication.- {3 ~( v. d5 ?1 k# T6 {/ J
( x, T7 }( q) C/ K2 |. `
7.6 Double-stranded RNA replication.' Q8 A' F6 z- m7 L6 h  G* V
, v) x! u: ]. t
7.7 Single-stranded RNA replication.
. H! C: B! V6 B" M" z
7.8 Reverse transcription.

8 Assembly and exit of virions from cells.

8.1 Introduction to assembly and exit of virions from cells.7 L4 m1 k6 \2 F
5 K! Z$ `+ L" q
8.2 Nucleocapsid assembly.0 k' @5 h& W( E. B, K8 D& h

8.3 Formation of virion membranes.  L: y7 R/ u2 K3 q1 j* }
: {+ m% z8 |0 ^3 {. t. `
8.4 Virion exit from the infected cell.5 b- \: e- Z+ }4 R
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9 Outcomes of infection for the host.3 w" R( @  `6 e6 z/ f

9.1 Introduction to outcomes of infection for the host.0 K3 e; I: _( }9 L1 T

9.2 Factors affecting outcomes of infection." r  A1 Q# O$ I* D' v5 D$ N
5 c( G8 |* t7 W5 _3 E( ~0 @
9.3 Non-productive infections.
8 k/ `3 m% K( X& ]6 T# i
9.4 Productive infections.$ P$ n8 M! x+ k/ w
. [/ R7 v3 a7 ~
10 Classification and nomenclature of viruses., ?( E* W/ Q; _

10.1 History of virus classification and nomenclature.
1 J/ {) P! w4 A' }$ p' {
10.2 Modern virus classification and nomenclature.

10.3 Baltimore classification of viruses.! O/ _; m4 U2 s: k& q: R* E5 O
6 F: V8 h' O+ x& r  `/ \' o
11 Herpesviruses (and other dsDNA viruses).

11.1 Introduction to herpesviruses.
- v: {0 W( i" U# s* q6 g
11.2 The human herpesviruses.
+ u( j" |' C8 R, B
11.3 The herpesvirus virion.) k2 L( S4 {& o
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11.4 HSV-1 genome organization.
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11.5 HSV-1 replication.

11.6 Latent herpesvirus infection.

11.7 Other dsDNA viruses.1 L& ?, @. `: p4 F7 v
, i) o0 O; [2 c: @1 P% d+ B9 |6 P
12 Parvoviruses (and other ssDNA viruses).4 Z' z1 |$ Z5 U) l- W

12.1 Introduction to parvoviruses.
# [+ J9 c" X# |$ _& y4 D
12.2 Examples of parvoviruses.

12.3 Parvovirus virion.- h4 @% |+ q6 C9 m4 g1 f7 D
8 x1 ^+ \0 @/ q3 T1 O
12.4 Parvovirus replication.

12.5 Other ssDNA viruses.

13 Reoviruses (and other dsRNA viruses).

13.1 Introduction to reoviruses.
9 p5 \, [) S% f5 |& Y! M. b
13.2 Rotavirus virion.% g6 Q- Z# N; H3 T3 `8 J
6 t) k/ j1 d! o& P4 M3 `
13.3 Rotavirus replication.

13.4 Other dsRNA viruses.7 s3 ~) x9 w# z1 k
2 s" i: ^0 d' H
14 Picornaviruses (and other plus-strand RNA viruses).
$ i  a& Z' F% w1 F, w6 X
14.1 Introduction to picornaviruses.

14.2 Some important picornaviruses.

14.3 The picornavirus virion.
0 t6 f( A) j& W+ a, z* c
14.4 Picornavirus replication., p$ R  p. A( {$ n* L

14.5 Picornavirus recombination.

14.6 Picornavirus experimental systems# y" O( {/ s+ p+ |

14.7 Other plus-strand RNA viruses.- \6 f4 i0 ]) H* J1 G# ?" p0 N
+ \8 t/ _$ y8 a( Z3 X
15 Rhabdoviruses (and other minus-strand RNA viruses).

15.1 Introduction to rhabdoviruses.- |& g* V. M! y: c( l

15.2 Some important rhabdoviruses.

15.3 The rhabdovirus virion and genome organization.9 b' A5 ~7 ^  _$ g
, e4 p  y/ L$ \6 i5 t  T
15.4 Rhabdovirus replication.% C1 i  E" I3 n7 ^$ x1 V6 @! B

15.5 Other minus-strand RNA viruses.

15.6 Viruses with ambisense genomes.# a- y8 d. n5 s* Y

15.7 Reverse genetics.9 ~" B0 e8 d/ @: z/ w1 }+ ^
( e  e: _2 C- X
16 Retroviruses./ d) ?" e7 l. T

16.1 Introduction to retroviruses.

16.2 Retrovirus virion.
4 y3 s: L+ U4 q$ }  J# N: Z7 j
16.3 Retrovirus replication.; x3 Y( t9 T: f; W) T

16.4 Examples of retroviruses.& g, @1 \/ l. ]4 G* w
* I1 k  M, I" n2 a; E
16.5 Retroviruses as gene vectors.

16.6 Endogenous retroviruses.1 _( J9 u# L, m) |' }5 p, y/ i

17 Human immunodeficiency viruses.1 r0 j2 E7 w# P
2 |6 j, m- e' ]7 Z7 E" h
17.1 Introduction to HIV.: f* e$ Q' z) x5 h
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17.2 HIV virion.0 ?# H1 x+ f7 |+ D: z

17.3 HIV genome.; _4 h7 R) v8 q8 \0 J4 ~
$ {/ |1 I# u! V' P2 y
17.4 HIV-1 replication.9 P3 w- R" u& X$ d& c" L# {" |

17.5 HIV-1 variability.

17.6 Progression of HIV infection.
8 @  b+ {- B, V7 v# A
17.7 Prevention of HIV transmission.6 J* i5 d$ d* {: M4 ~3 t% H% o3 O# f
& g, m: O2 i; J3 P6 S  p
18 Hepadnaviruses (and other reverse-transcribing DNA viruses)./ [! Q+ C8 x; {# V1 b8 ?: f

18.1 Introduction to hepadnaviruses.
5 w( v0 V* q$ j+ ?6 \
18.2 Importance of HBV.

18.3 HBV virion.) ~# T$ N3 a$ K* Q% B
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18.4 Non-infectious particles.
9 ^% ^" v6 i& H  s; I
18.5 Soluble virus protein.# |) U- J, v% j9 a! Q1 k: i

18.6 HBV genome.
. u; U. H, y: {! X/ A( t) ?, t
18.7 HBV genetic groups.

18.8 HBV replication cycle.0 g" M, ~1 L' o; X
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18.9 Prevention and treatment of HBV infection.) c, c4 p6 |% T$ F
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18.10 Other reverse-transcribing DNA viruses.

19 Bacterial viruses.3 R4 s7 y) I4 ?0 n- J' g

19.1 Introduction to bacterial viruses (bacteriophages.
6 z0 N! h3 ~& p
RNA PHAGES.9 @. k% E5 w' s: Y% ]4 |9 C; R; G

19.2 Single-stranded RNA phages.

19.3 Double-stranded RNA phages.9 V8 j. Y) x0 a/ Z1 g5 ]

DNA PHAGES.

19.4 Single-stranded DNA phages.
& X7 e" z( \) R" E3 l2 e* S
19.5 Double-stranded DNA phages.

20 Origins and evolution of viruses., x) Q* [. Q' }: \. k& K6 I
6 S8 I; Q" p3 {4 C
21.1 Introduction to origins and evolution of viruses.
' `) R' @  g: _6 }
20.2 Origins of viruses.* [, b0 ^2 F4 }- ^2 A6 j

20.3 Evolution of viruses.

21 Emerging viruses.

21.1 Introduction to emerging viruses
" X! P8 B( i. y7 }3 p
21.2 Viruses in new host species
! `0 |* T2 g7 Y0 _( x
21.3 Viruses in new areas

21.4 Viruses in new host species and in new areas
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21.5 New viruses1 k/ }; y0 i0 i* Q4 w$ h* K

21.6 Recently discovered virus; [6 ]6 H7 {# g: T/ W* K* v% R
6 x- ?; K7 j  S" c3 J+ h
21.7 Re-emerging viruses
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21.8 Virus surveillance/ S; i* C. `. R# p: O" b3 B
$ B* s8 [+ d2 U/ @; T. }
21.9 Dealing with outbreaks
- {/ X  ?& h/ I  Y+ S/ Z) g
22 Viruses and cancer' \2 {/ X7 n) j  k2 O1 }* V1 C) e

22.1 Introduction to viruses and cancer
; l0 {  t( J: D# D5 x5 Q4 ^
22.2 Papillomavirus-linked cancers$ ]; z# T6 b& V% Q# ~& e% z5 B

22.3 Polyomavirus-linked cancers6 V* B8 ^- c+ z2 `# a+ n: u
9 Q! l4 R; S5 X! z
22.4 Epstein-Barr virus-linked cancers7 y5 Q% x- [% h( O( g

22.5 Kaposi’s sarcoma
4 V% D7 I* R; v1 ~/ B6 d
22.6 Adult T cell leukaemia

22.7 Hepatocellular carcinoma* o6 \  e3 {. z9 M" q" V- H/ N
7 e. G# l- @4 m; P
22.8 Virus-associated cancers in animals

22.9 Cell lines derived from virus-associated cancers.
. N; Q+ G+ `4 ]7 x
22.10 How do viruses cause cancer?' a/ K5 [* ]% m! P* U5 K2 @

22.11 Prevention of virus-induced cancers.( r" v2 g: x: L6 J! e( h2 L
$ y1 Q; M% Y: c, w
23 Survival of infectivity.. o) ^0 C( t$ {0 r

23.1 Preservation of virus infectivity.

23.2 Destruction of virus infectivity.

23.3 Inactivation targets in virions.
% q5 Z! Q/ w2 ?
23.4 Inactivation kinetics.

23.5 Agents that inactivate virus infectivity.9 j$ X5 J' z( n/ r+ L+ |! F" h2 w

24 Virus vaccines.5 P* f) f/ S& U( v" J6 t% p
+ i9 v) Q, @$ X- e7 @
24.1 Introduction to virus vaccines.

24.2 Live attenuated virus vaccines.

24.3 Inactivated virus vaccines.0 ~# d: H7 L5 w, e3 q5 Z7 }7 H, w

24.4 Virion subunit vaccines.+ s5 {5 L# `0 T9 V

24.5 Live recombinant virus vaccines.( s8 J% A, ?4 P5 o4 O# j
; N1 l! }7 `9 m8 V, i  a" n
24.6 Mass production of viruses for vaccines.$ x3 V9 a: N9 T& B: d3 {

24.7 Virus-like particles.
% k* M- H! h+ k" J
24.8 Synthetic peptide vaccines.
; b4 {9 s% ~6 k
24.9 DNA vaccines.

24.10 Storage and transport of vaccines.) C# e8 b" l, S& H8 G( H

25 Anti-viral drugs.

25.1 Introduction to anti-viral drugs./ T* a- M6 U& z& u9 {0 Q

25.2 Development of anti-viral drugs.
7 ~. q  H8 {7 \
25.3 Examples of anti-viral drugs.0 b5 x7 s- i- M2 W7 C

25.4 Drug resistance.
. u. O: j0 G1 t# \7 _7 e
25.5 Anti-viral drug research.

26 Prions.! ^- [/ ?; k- i0 J" A) y- q! T
2 c% |7 W& u! p: s6 T
26.1 Introduction to prions.5 U# g1 ~( s( j
3 q5 P& M; {7 s+ k: k
26.2 Transmissible spongiform encephalopathies.% d# q, o" _9 F, u* U, U5 x' A% D
5 h/ M- u+ j- H. r* |, o, F
26.3 The nature of prions." f' [7 w3 R1 J7 O$ m

26.4 Prion diseases.

26.5 Prion strains.% P* ~! O5 _# e1 \0 W
. f! f) ]5 ]' f
26.6 Prion transmission.

26.7 The protein-only hypothesis.9 V$ F3 L; Z' l5 z- Q
  s: n3 Q# ?$ O  v+ h8 w" u3 i
Learning outcomes.0 ^$ o: I! h+ T% ], g! c4 [9 a( q
& `; b+ l, ^7 d' P
Sources of further information.
- V) S0 ~* m6 m' {* }, P9 i
Virologists' vocabulary.5 B( ]* ?8 A# D  \  l- K

Index.

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