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Virology - Principles and Applications1 q5 X2 c' I# a  |- x% ?6 i
Dr John Carter (Liverpool John Moores University, UK), Prof Venetia Saunders (Liverpool John Moores University, UK): B$ B$ W4 A- W& s$ D6 I6 D. Y: _
August 2007, ©2007
by Dr John Carter, Prof Venetia Saunders5 O& J, }8 y- a- W8 ]/ L
ISBN 978-0-470-02387-7
Preface." X% N2 F) L+ z2 b8 ?; j/ A
$ r5 I0 a, O) X' X( @
Abbreviations used in this book.
, @+ w3 C! p/ ^$ X' l
Greek letters used in this book.
- ]3 ~: ?, O1 Y9 w/ f
Colour coding for molecules.
2 f2 {# K2 ]: x
1 Viruses and their importance.
1 u" |3 I+ {: ?2 n" }: a
1.1 Viruses are ubiquitous on Earth.* H3 }2 l9 K/ `. ]
- v9 \$ d1 T; \4 ?
1.2 Reasons for studying viruses.& g# B2 U3 m# p3 A$ z2 v

1.3 The nature of viruses.

1.4 The remainder of the book.

2 Methods used in virology.

2.1 Introduction to methods used in virology.! z4 e9 A8 Z6 D2 f( J

2.2 Cultivation of viruses.9 I8 f4 u7 x3 F5 _" w" w2 }

2.3 Isolation of viruses.
# r* h0 ?3 l. f3 p  u5 P  P: x
2.4 Centrifugation.) _4 r9 ~$ ]8 w3 J

2.5 Structural investigations of cells and virions.
3 F% D) l2 u! H1 i1 Y9 y( w
2.6 Electrophoretic techniques.3 P/ h5 J! }& m
- I5 W& F7 j6 X4 K8 d
2.7 Detection of viruses and virus components.

2.8 Infectivity assays.7 |0 U0 D, ?4 t8 c$ i- V* O8 x. Y  |
1 Z4 K+ C/ m% Y8 Y
2.9 Virus genetics.' P' K$ s1 b5 m7 x9 C

3 Virus structure.3 o1 e: j# f: `$ p* q

3.1 Introduction to virus structure.; ^9 Y2 Q# T& M1 T$ ?& |
3 W- n; s. {* g; C2 W/ Q
3.2 Virus genomes.: h  u, b2 ?: E$ x
) l% f1 P: Z  P& e. {
3.3 Virus proteins.
9 ~, m1 F- a  A9 g4 g2 F7 `
3.4 Capsids.! T7 l# O2 Y& U* u4 H7 W# {& {) T
& E3 N7 |# K4 G+ S: r4 W5 s
3.5 Virion membranes.
" n' x7 R" ]. n' i7 x, `1 o4 `0 h% b# e
3.6 Occlusion bodies.( R' B# j( n8 t( _. J! ?) Q

3.7 Other virion components.% U; p9 U# X! w9 G% q0 i- M/ s
. i: ?" W* l0 C' V; O: b, U. J
4 Virus transmission.. }& \" Y/ h$ Z& E) C$ X# D% M
+ \, P$ {. V0 u0 ]5 n  R' P
4.1 Introduction to virus transmission.! n& F7 l! ~4 c) M7 N3 s

4.2 Transmission of plant viruses.
& g, }# y) u: q1 o% ~. n, B  R6 m
4.3 Transmission of vertebrate viruses.

4.4 Transmission of invertebrate viruses.8 [8 P7 m; G  W; Z2 V

4.5 Permissive cells.
% O9 {+ s0 A! d( P0 {- Y0 h! T
5 Attachment and entry of viruses into cells.; _6 d" M* h0 ^

5.1 Overview of virus replication.
& a; i, q1 ]2 W  y/ p- a4 P
5.2 Animal viruses.! p4 Y1 K" u3 O, P9 U- g, B: b: X( T& x

5.3 Bacteriophages.& l& A8 ~+ c( E
$ s" L& l  {0 ]# \
6 Transcription, translation and transport.

6.1 Introduction to transcription, translation and transport.
; }* V* Y) h4 V0 ~) `. \6 m
6.2 Transcription of virus genomes.

6.3 Transcription in eukaryotes.

6.4 Translation in eukaryotes.
( M' e* i' t  Q! u: K
6.5 Transport in eukaryotic cells.
" o" T8 T8 R4 ~1 a$ M
6.6 Transcription and translation in bacteria.
8 v5 h) d8 w0 Y4 x; T' d6 ]
7 Virus genome replication.
( Y3 c* l5 h& B
7.1 Overview of virus genome replication.4 x5 H) Q! V0 @$ f1 [% v( O

7.2 Locations of virus genome replication in eukaryotic cells./ K9 N0 o9 Y2 S* |* G/ O0 S6 p/ d
( i, r% _; i# s5 b: \- ]4 r$ N
7.3 Initiation of genome replication.5 }% ~, |! V, d8 o* x( n

7.4 Polymerases.
  f8 W5 O9 R8 X$ S& e- y
7.5 DNA replication.: R0 r1 g% m% v7 W" w  a

7.6 Double-stranded RNA replication.% g5 a; h+ B) S/ t2 w8 u- O* g
$ x$ q5 n4 J% N
7.7 Single-stranded RNA replication.

7.8 Reverse transcription.

8 Assembly and exit of virions from cells.
* }* a( ?' F  c" O5 b6 F+ G
8.1 Introduction to assembly and exit of virions from cells.
' _+ a, Q; ?: z& ]2 F# w! j; ~, K( a
8.2 Nucleocapsid assembly.& A  g+ o) ~* r/ l; F

8.3 Formation of virion membranes.% n" ^! L/ i* r' J% N

8.4 Virion exit from the infected cell.1 M2 ]4 V! q/ v2 _' @. S

9 Outcomes of infection for the host.
/ Z" z4 ?/ C, u/ _7 {6 ^
9.1 Introduction to outcomes of infection for the host.% Y- j- T1 Q7 r9 Z# M

9.2 Factors affecting outcomes of infection.5 G( `8 T- l& J1 O

9.3 Non-productive infections.

9.4 Productive infections.3 }$ Z1 n0 z" p0 d5 a; b

10 Classification and nomenclature of viruses.8 J  ?9 p; b4 b5 Q
5 d: d- P1 }7 X
10.1 History of virus classification and nomenclature.
! w% T0 V& B  l. d
10.2 Modern virus classification and nomenclature., e2 _. J0 e, V% @$ e2 F# X

10.3 Baltimore classification of viruses.! F+ J! n- A3 e  C3 A% N

11 Herpesviruses (and other dsDNA viruses).
5 [* U( k2 E4 q* Y  G4 q
11.1 Introduction to herpesviruses.
2 K5 P' U) Z& C5 R/ o% a7 Y* c4 k
11.2 The human herpesviruses.

11.3 The herpesvirus virion.+ N" e1 D( s' }. M1 e

11.4 HSV-1 genome organization.

11.5 HSV-1 replication.

11.6 Latent herpesvirus infection.# O8 U1 o. h2 y# A% {# u
8 G1 E* Y5 x& x  x; `2 e
11.7 Other dsDNA viruses.
8 q& h4 g4 s9 t0 c+ G) |" c
12 Parvoviruses (and other ssDNA viruses).

12.1 Introduction to parvoviruses.

12.2 Examples of parvoviruses.: e, x! d) X" F) q

12.3 Parvovirus virion.' [* E# }* T' s8 ~5 M0 q

12.4 Parvovirus replication.
; A3 p8 \* f5 h, c4 U7 B1 v
12.5 Other ssDNA viruses.
$ ~6 O6 z, j4 B5 E- d5 c, ~
13 Reoviruses (and other dsRNA viruses).
/ x+ M! g6 k  }5 E  U* U
13.1 Introduction to reoviruses./ G5 @1 l1 E6 F9 o9 p

13.2 Rotavirus virion.
8 w2 j: u: V2 k6 f, @
13.3 Rotavirus replication.% E4 T: }2 Q& f7 C/ m$ d0 f
. m5 l! Z8 ^# K0 k" n
13.4 Other dsRNA viruses.) g% E- A5 E; ]. M
+ l" Q9 R' ]/ j" N
14 Picornaviruses (and other plus-strand RNA viruses).' s1 ]: F4 t) X0 }
% V' m  J8 P! j  C* m9 m
14.1 Introduction to picornaviruses.

14.2 Some important picornaviruses.1 J* C! k0 N8 X$ B
6 i8 C2 M; b: `2 m4 z
14.3 The picornavirus virion.2 O2 f/ q" K7 W

14.4 Picornavirus replication.

14.5 Picornavirus recombination.
! x' e8 c8 ]' O" i3 X4 W5 E& o
14.6 Picornavirus experimental systems
- q2 ^" I4 I& }* @8 i1 ~5 A
14.7 Other plus-strand RNA viruses.

15 Rhabdoviruses (and other minus-strand RNA viruses).

15.1 Introduction to rhabdoviruses.
; g4 r' ?/ Q0 s+ C: d: K
15.2 Some important rhabdoviruses.

15.3 The rhabdovirus virion and genome organization.: T- B! O) d1 U9 ]! g

15.4 Rhabdovirus replication.9 V" B& L7 p$ u0 S: y" y
3 M- b/ W, _. Z, o
15.5 Other minus-strand RNA viruses.
6 N$ ^# j4 @  e. Z. ~
15.6 Viruses with ambisense genomes.

15.7 Reverse genetics.

16 Retroviruses.
; b+ `# K" D7 C' z$ ]" a
16.1 Introduction to retroviruses.: @, |# m" u* `
" L8 d" n7 |% t. e; q3 T
16.2 Retrovirus virion.1 `! \# }5 g# o0 T
; {% D6 x# x# x/ R* e
16.3 Retrovirus replication.: w3 h1 O8 D4 h: z) R+ K
' W/ e/ s! m8 G! Q  T
16.4 Examples of retroviruses.
/ U: R) Z$ y  l, U7 r
16.5 Retroviruses as gene vectors.
1 [# x. [" M1 v& S; Q# O8 v
16.6 Endogenous retroviruses.

17 Human immunodeficiency viruses.
* ?" u* H) ]1 h' a0 k
17.1 Introduction to HIV.

17.2 HIV virion.

17.3 HIV genome.

17.4 HIV-1 replication.

17.5 HIV-1 variability.

17.6 Progression of HIV infection.- t, N; X4 c, k5 Z

17.7 Prevention of HIV transmission.

18 Hepadnaviruses (and other reverse-transcribing DNA viruses).

18.1 Introduction to hepadnaviruses.$ d- w9 \( V% {: e' ~; \

18.2 Importance of HBV.
4 K2 n/ F, f7 ~4 P, P
18.3 HBV virion.

18.4 Non-infectious particles.
6 b% n8 y( s! Z# b2 [& {! w
18.5 Soluble virus protein.+ f; T& B) z9 g0 ]2 W$ c

18.6 HBV genome.

18.7 HBV genetic groups.% A% s  r4 `: S* F: s6 |

18.8 HBV replication cycle.

18.9 Prevention and treatment of HBV infection." X) \- V/ y0 u* a

18.10 Other reverse-transcribing DNA viruses.! g) C. c" b2 a: P7 D& K

19 Bacterial viruses.

19.1 Introduction to bacterial viruses (bacteriophages.( d" ]# h% T8 V# T

RNA PHAGES.: o5 G2 O$ G1 Q+ q  h& p" n( $ R, r

19.2 Single-stranded RNA phages.4 ~% C9 r3 ?1 K) u
% L, w) `6 i. v/ s- O! B' M
19.3 Double-stranded RNA phages.& }8 A) E+ u$ i
! t2 ?. s9 y( E; k0 O
DNA PHAGES.$ O, R5 k# Z, B5 L+ k: Y' g
/ U! s0 G! g2 W' k/ Q  Q
19.4 Single-stranded DNA phages.
& B" l/ t/ p+ N6 a
19.5 Double-stranded DNA phages.8 v+ }6 j9 l/ y# N

20 Origins and evolution of viruses.
: x0 V) h2 l! C' K( r! u- T
21.1 Introduction to origins and evolution of viruses.
  h& k% |% l' i* R* q
20.2 Origins of viruses.4 ]) s% w& w) t. i
0 P  W% K# f0 [& g* i
20.3 Evolution of viruses.! V; M" t: \* k" y8 i
1 r/ O) ]# L% e1 G& p( ^
21 Emerging viruses.: z. J  _, u3 Z7 R5 r4 D' U
5 v7 F2 a4 `7 m& p7 o5 O/ s
21.1 Introduction to emerging viruses, S! t+ }4 a9 }+ Z  _/ r8 w

21.2 Viruses in new host species
& w( [% ?) z5 B- l
21.3 Viruses in new areas& F. w( I' p. b. j, d' E5 i
. r; ^5 i! ~: W2 x% K
21.4 Viruses in new host species and in new areas- m4 L: N; D- b3 r- g. e
! a5 I5 x; $ F; W' }
21.5 New viruses

21.6 Recently discovered virus
+ Z* i) C6 ^: B
21.7 Re-emerging viruses

21.8 Virus surveillance
, a) N" t" D9 z- M0 A( J
21.9 Dealing with outbreaks

22 Viruses and cancer- P( s$ g5 `1 ?3 S4 T

22.1 Introduction to viruses and cancer
% |2 X; |( Z: S' Z& t
22.2 Papillomavirus-linked cancers
  R0 G- P7 s! L7 ~6 V# v. v
22.3 Polyomavirus-linked cancers9 a8 X9 o, j3 m# r/ P1 k' _
% c6 s3 K3 ?. S, r
22.4 Epstein-Barr virus-linked cancers' d. G" b6 l+ N( F
0 A: a% r0 Z9 l/ g
22.5 Kaposi’s sarcoma. H6 M; ^6 V) }

22.6 Adult T cell leukaemia

22.7 Hepatocellular carcinoma3 a4 n% Z: h2 U
) M+ A3 b, j4 N
22.8 Virus-associated cancers in animals: @. X, V+ T0 y
& F: n7 _! M: g! v+ {) _
22.9 Cell lines derived from virus-associated cancers.
6 m& C1 z4 p- \& |& j- p
22.10 How do viruses cause cancer?

22.11 Prevention of virus-induced cancers.

23 Survival of infectivity.) g' h& f+ J# D  I1 T

23.1 Preservation of virus infectivity.
/ _( D8 B- z5 M7 j& ^/ i2 }& x
23.2 Destruction of virus infectivity.
" |4 C6 L; {: o6 |: n
23.3 Inactivation targets in virions.

23.4 Inactivation kinetics.

23.5 Agents that inactivate virus infectivity.
$ C! z. k# g' v7 `7 n& I( k
24 Virus vaccines.+ _# P+ Q9 f* |: Q

24.1 Introduction to virus vaccines.' b- o; P6 ?* m% ~% N

24.2 Live attenuated virus vaccines., Q# H% D' w5 Z- x

24.3 Inactivated virus vaccines.

24.4 Virion subunit vaccines., ^( k4 I0 }7 a- s6 ?- O' h: z
0 o, L( f3 }8 U' n" h- p! }
24.5 Live recombinant virus vaccines.  f( C6 H6 P, H4 C. R
) Q4 \' O1 {" C
24.6 Mass production of viruses for vaccines.

24.7 Virus-like particles.% w) s. W0 s. v. n" {
8 V' ]0 w# {% f
24.8 Synthetic peptide vaccines.1 k5 [, t0 z& v4 t
, \/ o$ H9 z# u& ^0 @" Y/ m
24.9 DNA vaccines.

24.10 Storage and transport of vaccines.

25 Anti-viral drugs.0 W$ C0 b% L, t
) S$ _/ G3 v$ z/ k8 p
25.1 Introduction to anti-viral drugs.
, c% D* t  L9 a' `
25.2 Development of anti-viral drugs.1 {+ G9 K; _! \9 c! e6 t
( \) e" b$ I+ V
25.3 Examples of anti-viral drugs.% e/ l* k, D, ~$ L
5 U% f7 ^+ m; R4 X+ M1 Y  y
25.4 Drug resistance.( ^' g6 [& k1 g! [) I' B

25.5 Anti-viral drug research.

26 Prions.* y  x+ L& K, H) l# u

26.1 Introduction to prions.

26.2 Transmissible spongiform encephalopathies.

26.3 The nature of prions.7 o# }! i% C  `+ b, A) H

26.4 Prion diseases.

26.5 Prion strains.1 z7 m6 r" u* m4 G- a

26.6 Prion transmission.
$ A) i6 R% I7 U: m* e5 i. Z
26.7 The protein-only hypothesis.

Learning outcomes.
9 P$ C( C3 y2 `' ^
Sources of further information.' C9 e" `$ r0 S% z9 ?

Virologists' vocabulary.

Index.

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