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Virology - Principles and Applications
Dr John Carter (Liverpool John Moores University, UK), Prof Venetia Saunders (Liverpool John Moores University, UK)
August 2007, ©20076 o3 M. P$ Z: x- |. y8 K
by Dr John Carter, Prof Venetia Saunders
ISBN 978-0-470-02387-7$ P" ?( F, n$ C6 y
Preface.
% T$ B- J5 S/ ]& R8 G) e
Abbreviations used in this book.

Greek letters used in this book.
+ e1 A. U% R& r
Colour coding for molecules., U0 g/ `+ i: B1 p
" p+ m$ w' X) H0 h
1 Viruses and their importance.' v- u% w4 @+ P9 Y
& r5 Q8 l$ B% x$ F) R, ]7 ^* L
1.1 Viruses are ubiquitous on Earth.% {: T# K) C: w0 p

1.2 Reasons for studying viruses.8 S! p2 B, p. s& V
& u2 H. z3 b% F- y6 C' |, L* R: Y
1.3 The nature of viruses.

1.4 The remainder of the book.

2 Methods used in virology.
; c! M7 g* I  c
2.1 Introduction to methods used in virology.$ X0 l% P8 h# K2 }/ U
/ D. X5 n' Z3 T7 Y2 A
2.2 Cultivation of viruses.( Z8 A9 Y% y4 n. x

2.3 Isolation of viruses.$ j4 M% [; }6 ~+ n) D$ V( e

2.4 Centrifugation.) q6 K, X: y: ?9 ^" i* l

2.5 Structural investigations of cells and virions.

2.6 Electrophoretic techniques.# l. Q3 Y: Y$ ?

2.7 Detection of viruses and virus components.0 P- p* t! g' m2 a
8 N6 G( l$ |- y. m1 \* q6 ~  _
2.8 Infectivity assays.
# Z- Y8 b1 a" N  t
2.9 Virus genetics.

3 Virus structure.6 q  f; e5 @1 b. I: ^
" y) D8 Q# P/ Y' S6 w4 t
3.1 Introduction to virus structure., ~$ H! p8 [" Q. D  @6 ?  U
& R5 ^8 h, p4 `: {) g
3.2 Virus genomes.

3.3 Virus proteins.
4 x+ y3 v" B, U
3.4 Capsids.4 c; U$ I, @7 E0 P' g; X7 j

3.5 Virion membranes.6 r: i+ d0 e( ^' K5 I; t+ s
" C( Y$ M; b/ J; P  }1 I
3.6 Occlusion bodies.
8 V& F: l2 U/ _* ?/ N6 f
3.7 Other virion components.+ a" H) ?# g: q) A/ h

4 Virus transmission.

4.1 Introduction to virus transmission.

4.2 Transmission of plant viruses.1 M; ^, C" e( z" n  z

4.3 Transmission of vertebrate viruses." p% Z- h$ ]9 C* n

4.4 Transmission of invertebrate viruses.
. n5 {: f8 P% l( X3 H
4.5 Permissive cells.

5 Attachment and entry of viruses into cells.! x% f0 o( h/ j* d" y: [" ]2 M: B
0 z4 M6 Y: _/ r- V' S2 j
5.1 Overview of virus replication.
! h8 _% d9 s. @+ X  E
5.2 Animal viruses.8 o) _9 c; `/ G, k# f9 f
; H- w. K3 \& m5 B" b
5.3 Bacteriophages.
& {0 k% ~; b3 b" l
6 Transcription, translation and transport.

6.1 Introduction to transcription, translation and transport.
! d1 b/ s  s9 u! N4 U
6.2 Transcription of virus genomes.8 X% P, V0 P# H' K; k1 e2 w7 D+ ~
9 n2 u$ b7 Y: b& `* v9 b4 p
6.3 Transcription in eukaryotes.: A; W3 R& M7 ?) z; F, p

6.4 Translation in eukaryotes./ }" N+ a+ B# e

6.5 Transport in eukaryotic cells., _) X; X: b4 a/ R" ~4 I& G
0 `! B, d* O" b9 r1 f
6.6 Transcription and translation in bacteria.

7 Virus genome replication.
- @/ d' C' O' X7 B' d% H
7.1 Overview of virus genome replication.

7.2 Locations of virus genome replication in eukaryotic cells.
1 S8 H3 X* n, q; i! _
7.3 Initiation of genome replication.' a0 L# v% L# g+ l
) P# u) S; B  L  T! @
7.4 Polymerases.

7.5 DNA replication.

7.6 Double-stranded RNA replication.

7.7 Single-stranded RNA replication.# g4 n/ L  R& r, U0 q

7.8 Reverse transcription.
1 j: N# d6 U# g8 l+ Q6 S% I3 J
8 Assembly and exit of virions from cells.9 f+ h; a5 w3 e, g

8.1 Introduction to assembly and exit of virions from cells.
# @# G# ^5 E3 D4 O
8.2 Nucleocapsid assembly." b0 D2 ]7 U# z! E
1 M2 y: d3 x% L9 r7 @3 i3 I
8.3 Formation of virion membranes.

8.4 Virion exit from the infected cell.

9 Outcomes of infection for the host.( J5 M1 k& ]3 V& V, E8 O1 j9 \

9.1 Introduction to outcomes of infection for the host.3 S, N9 r1 z0 U2 }  Y- r2 r  M

9.2 Factors affecting outcomes of infection.( J! U! V! i, K" }6 q0 Y

9.3 Non-productive infections.: j3 T1 @, ^( V9 d

9.4 Productive infections.

10 Classification and nomenclature of viruses.0 i6 d* u9 i( K1 H& ?: n1 X" B

10.1 History of virus classification and nomenclature.) B. O* u5 g% a) @

10.2 Modern virus classification and nomenclature.
% o" f* @: n8 ?( u6 {9 D
10.3 Baltimore classification of viruses.
; Z/ g% x& s/ d$ q- g  q
11 Herpesviruses (and other dsDNA viruses).
, {6 F" W$ @% E$ Q" d8 m
11.1 Introduction to herpesviruses.
8 t& z1 K) I1 n; h
11.2 The human herpesviruses.
5 \. [7 R# {" e- U6 w: y. l' q
11.3 The herpesvirus virion.

11.4 HSV-1 genome organization.

11.5 HSV-1 replication.
) l% T0 L4 e+ U* z1 Y
11.6 Latent herpesvirus infection.+ e" o- k/ ~6 f: d! L

11.7 Other dsDNA viruses.

12 Parvoviruses (and other ssDNA viruses).8 @5 r8 f: y( T6 H& D' G" R

12.1 Introduction to parvoviruses.

12.2 Examples of parvoviruses.
0 @) F( p, {: c4 e3 U( w. o
12.3 Parvovirus virion.3 y2 j; R, L# S- y4 R3 @
2 ]' \$ u8 A0 I
12.4 Parvovirus replication.2 }4 j$ e' V% v5 c+ f# m0 o

12.5 Other ssDNA viruses.
) j* Z: ]1 u, R+ x$ r
13 Reoviruses (and other dsRNA viruses).
( d8 }4 R) B$ @3 @5 G2 m9 h
13.1 Introduction to reoviruses.
9 r$ k" s# T; J. g7 b! q
13.2 Rotavirus virion.. V% P! _9 Z) y
4 }3 G: \9 e2 n0 Q6 A+ O! S- H
13.3 Rotavirus replication.

13.4 Other dsRNA viruses.
% Z3 _8 B1 o, C1 j$ ?( L% m) b
14 Picornaviruses (and other plus-strand RNA viruses).9 T) A5 t1 q2 a$ i( s3 ^& s

14.1 Introduction to picornaviruses.

14.2 Some important picornaviruses.

14.3 The picornavirus virion." I1 a6 ]8 g! X, W

14.4 Picornavirus replication.1 d2 C$ Z' d5 e/ B6 `. S

14.5 Picornavirus recombination.

14.6 Picornavirus experimental systems* E# L, I; n2 H- i  M  u
: _8 Z- G! q0 k5 K& B3 ?
14.7 Other plus-strand RNA viruses.# h. z& O# z& x9 Z; S* p0 }* `4 \

15 Rhabdoviruses (and other minus-strand RNA viruses).
; |- S! x$ q  L3 S8 |0 I
15.1 Introduction to rhabdoviruses./ z; F4 U# I' F4 v  b' A# d

15.2 Some important rhabdoviruses.( D9 h2 q& Q# j. V! F( i2 M1 A0 W

15.3 The rhabdovirus virion and genome organization.
# n1 p, Y( r# x* h0 k# {
15.4 Rhabdovirus replication.
" |3 j% @; d& h6 q- E( o
15.5 Other minus-strand RNA viruses.

15.6 Viruses with ambisense genomes.

15.7 Reverse genetics.* \1 _' @5 ^; s8 u% {1 O" e, H+ G

16 Retroviruses.

16.1 Introduction to retroviruses./ ]4 t& J; H( y; S
3 S1 Z2 B- i1 J% ~/ ^/ R
16.2 Retrovirus virion.; g& L9 r( P" U% s  D& s/ b

16.3 Retrovirus replication.
$ k8 F( t! d4 a5 T/ b" `
16.4 Examples of retroviruses.
, `6 N9 U) k4 `5 s9 f, e/ }1 m
16.5 Retroviruses as gene vectors.; Z# g: S% j8 W1 y
! T) ^/ {4 O) R
16.6 Endogenous retroviruses.& B: v! d4 P0 A1 p1 a

17 Human immunodeficiency viruses.3 L% u6 b1 U# C* D; g
& f3 ]2 ?# j% G& A- D  G* e
17.1 Introduction to HIV.9 ]& R1 S+ O- E0 {
3 g, i% q7 W! C# k& v  `
17.2 HIV virion." [0 o0 E  Y5 F9 m/ j1 O. g" c

17.3 HIV genome.

17.4 HIV-1 replication.

17.5 HIV-1 variability.

17.6 Progression of HIV infection.
3 y4 B$ C2 f* C' y* \9 u) s
17.7 Prevention of HIV transmission.

18 Hepadnaviruses (and other reverse-transcribing DNA viruses).
- b# `) \# Y0 U8 A
18.1 Introduction to hepadnaviruses.1 C1 g' k) p, M  {+ n- n' {
* B/ }, d# e3 h. f3 q+ z
18.2 Importance of HBV." L6 J) U2 ]$ j5 b1 d+ K& a
' {8 f9 v+ ]4 ?8 N/ Y" s
18.3 HBV virion.
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18.4 Non-infectious particles.) H$ E8 ]! d$ w

18.5 Soluble virus protein.
# |" y2 e" |: x) x3 W: x% g
18.6 HBV genome.( ], I, W( J" V  o7 C
7 n1 Q( w" Q7 h
18.7 HBV genetic groups.3 g1 B1 g6 z, W1 Z. s9 g' j
/ e: q/ N& q* W4 A& A  B
18.8 HBV replication cycle.7 {6 K! j$ m2 z1 a" l) I$ b

18.9 Prevention and treatment of HBV infection.' w+ ], e, q. T5 n' z( {  F5 n1 {
* F  L7 S, W4 F  S. |
18.10 Other reverse-transcribing DNA viruses.$ M4 y0 I, g1 g+ m" ^( g
9 C4 ]0 x& L  C  I0 O! H
19 Bacterial viruses.

19.1 Introduction to bacterial viruses (bacteriophages.* b$ X2 o8 E) W4 J. z( ^

RNA PHAGES.
( I+ Z5 k% x( C; |2 z) C
19.2 Single-stranded RNA phages.- v" t. E) I9 V: N4 D

19.3 Double-stranded RNA phages.

DNA PHAGES.& H- q, ]& y# F3 J, ?& t

19.4 Single-stranded DNA phages.( R  l" x$ Z& Y0 M7 z9 t

19.5 Double-stranded DNA phages.9 j, Y4 J0 B' X) s& S
. u% i" P; @" }3 e# c" R
20 Origins and evolution of viruses.
3 ~$ B, g. S0 p" T8 q$ t
21.1 Introduction to origins and evolution of viruses.3 Q; G2 R. O8 @' J
" }8 T! i9 I5 K/ C+ I  z
20.2 Origins of viruses., |2 _$ Y+ m! B( n: }
; [) F7 O; j2 ~. V1 X% C
20.3 Evolution of viruses.
0 g; g- c# H9 h% W8 k
21 Emerging viruses.+ Q8 \) A! H! }' h
7 @! Q2 H* }7 b9 W
21.1 Introduction to emerging viruses# X# W. B2 |( \8 G3 @
% ~' b  q8 N* L& P$ }
21.2 Viruses in new host species
4 R% X/ x0 a2 T# v$ Y" u
21.3 Viruses in new areas
8 l4 C/ H( J" [1 V# l/ R# p/ n/ n
21.4 Viruses in new host species and in new areas
" ^( O1 s; H4 ?1 a
21.5 New viruses
  K' j5 @. ^: L! |/ ~
21.6 Recently discovered virus

21.7 Re-emerging viruses

21.8 Virus surveillance

21.9 Dealing with outbreaks
4 \4 x. F7 ]: d
22 Viruses and cancer
6 @9 E, M$ m$ |
22.1 Introduction to viruses and cancer0 X/ E* I, b  N# h. E

22.2 Papillomavirus-linked cancers
4 r4 g% a; D# o0 O
22.3 Polyomavirus-linked cancers
4 X' p7 F  j/ [# N3 [! P
22.4 Epstein-Barr virus-linked cancers
; o/ M( e* q; C( z; @
22.5 Kaposi’s sarcoma3 [' H) _2 z; q  ^- N( {
$ c0 w) R& H+ V7 b
22.6 Adult T cell leukaemia
* h# h& n5 g; v; I/ Y
22.7 Hepatocellular carcinoma. W- C% D$ r4 I& S8 i

22.8 Virus-associated cancers in animals2 p  o# U" E2 F, Q( Y; \$ Y

22.9 Cell lines derived from virus-associated cancers.
% _* K( `7 i/ k- H8 d
22.10 How do viruses cause cancer?/ a) d, L# p) A# m2 {
1 ~# _: y  i6 [" Z
22.11 Prevention of virus-induced cancers./ g* s4 \# y5 Q6 ]9 G9 O
4 }2 I, w& G) ^% q2 M, U2 b
23 Survival of infectivity.

23.1 Preservation of virus infectivity.

23.2 Destruction of virus infectivity.4 ]: n: G* k- f# I0 ?) [
. z% _/ V  G' Z# ~/ W7 q& ]
23.3 Inactivation targets in virions.- x$ o- s. A2 d  k& D: h& V9 S

23.4 Inactivation kinetics.+ U% N) }( z( H6 y
2 D7 A+ p0 R6 ^; a: g" u
23.5 Agents that inactivate virus infectivity.

24 Virus vaccines.

24.1 Introduction to virus vaccines.

24.2 Live attenuated virus vaccines.. O1 M% m  ^5 t' ~: h$ e

24.3 Inactivated virus vaccines.
% j# K+ u6 L8 Q9 P
24.4 Virion subunit vaccines.

24.5 Live recombinant virus vaccines.

24.6 Mass production of viruses for vaccines.& l7 p" B8 |- X3 F  f6 B2 a

24.7 Virus-like particles.2 [* @) t* R* t; w

24.8 Synthetic peptide vaccines.

24.9 DNA vaccines.3 E& @# i- |; b! V9 h
3 D/ r8 \( B5 n. t0 b
24.10 Storage and transport of vaccines.; G5 f) I1 q) A# ~& ?! I

25 Anti-viral drugs.
' P1 t$ T$ |" n9 y6 l1 Z
25.1 Introduction to anti-viral drugs.1 `$ O3 J" T+ w
8 ]) |3 U  F9 L, b! f
25.2 Development of anti-viral drugs.* Z3 N  h) \! @! t) j
) D1 }9 M  ?7 K( Q+ a
25.3 Examples of anti-viral drugs.

25.4 Drug resistance.7 ?  U8 b2 o7 c* f9 z: G! g# x

25.5 Anti-viral drug research.
; p0 l2 r' ^4 e8 R5 x
26 Prions.
9 w7 }8 c$ i7 {" m/ ^
26.1 Introduction to prions.; v# J% q" q; \( C' d& z
( U* n0 T# l; S  ^. ?* M9 W* [
26.2 Transmissible spongiform encephalopathies.

26.3 The nature of prions.
# e0 e) v+ U2 w* ^3 P  N, S. m' `
26.4 Prion diseases.5 ~' d9 l# p9 O! N3 O9 U% [* J

26.5 Prion strains.

26.6 Prion transmission.4 H/ P3 ^6 w5 ~6 l$ B

26.7 The protein-only hypothesis.1 M8 ?0 a3 I2 Y8 ]2 M
) D  o4 _! }& `2 C1 }' L
Learning outcomes.. {3 S3 x  M3 `" E, \6 c8 y
8 y5 f4 E; G7 J: H! J, X
Sources of further information.0 i0 K5 ~/ M) _. ?% o( i& T
# |3 s8 ?' N$ G) V
Virologists' vocabulary.8 I6 e/ t4 `" }9 c3 q

Index.

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