This document discusses viral replication. It begins by defining viruses and their basic components. Viruses replicate through an intracellular process that involves attaching to and entering a host cell, uncoating their genome, expressing genes, replicating their genome, assembling new virions, and exiting the host cell. The replication process varies between virus families but generally follows these basic steps. Viruses are classified based on characteristics like their nucleic acid, replication strategy, and presence of an envelope.

1. Viral replication
• Overview
A virus is an infectious agent that is minimally
constructed of two components: 1) a genome
consisting of either ribonucleic acid (RNA) or
deoxyribonucleic acid (DNA), but not both, and
2) a protein-containing structure (capsid)
designed to protect the genome (Figure 23.1A).

2. • Many viruses have additional structural
features, for example, an envelope composed
of a protein-containing lipid bilayer, whose
presence or absence further distinguishes one
virus group from another (Figure 23.1B). A
complete virus particle combining these
structural elements is called a virion.

3. • In functional terms, a virion can be envisioned
as a delivery system that surrounds a nucleic
acid payload. The delivery system is designed
to protect the genome and enable the virus to
bind to host cells. The payload is the viral
genome and may also include enzymes
required for the initial steps in viral
replication—a process that is obligately
intracellular.

4. • The pathogenicity of a virus depends on a
great variety of structural and functional
characteristics. Therefore, even within a
closely related group of viruses, different
species may produce significantly distinct
clinical pathologies.

6. • Characteristics Used to Define Virus Families,
Genera, and Species
• Viruses are divided into related groups, or
families, and, sometimes into subfamilies based
on:
• 1) type and structure of the viral nucleic acid,
• 2) the strategy used in its replication,
• 3) type of symmetry of the virus capsid (helical
versus icosahedral), and 4) presence or absence
of a lipid envelope.

7. • Within a virus family, differences in additional
specific properties,
• such as host range, serologic reactions,
• amino acid sequences of viral proteins,
• degree of nucleic acid homology, among
others, form the basis for division into genera
(singular = genus) and species (Figure 23.2).

8. • Species of the same virus isolated from
different geographic locations may differ from
each other in nucleotide sequence. In this
case, they are referred to as strains of the
same species.

9. • Viral Replication: the One-Step Growth Curve
• The one-step growth curve is a representation
of the overall change, with time, in the
amount of infectious virus in a single cell that
has been infected by a single virus particle.

10. • In practice, this is determined by following
events in a large population of infected cells in
which the infection is proceeding as nearly
synchronously as can be achieved by
manipulating the experimental conditions.

11. • Whereas the time scale and yield of progeny
virus vary greatly among virus families, the
basic features of the infectious cycle are
similar for all viruses. The one-step growth
curve begins with the eclipse period, which is
followed by a period of exponential growth
(Figure 23.7).

12. • Eclipse period
Following initial attachment of a virus to the
host cell, the ability of that virus to infect other
cells disappears. This is the eclipse period, and it
represents the time elapsed from initial entry
and disassembly of the parental virus to the
assembly of the first progeny virion

13. • During this period, active synthesis of virus
components is occurring. The eclipse period
for most human viruses falls within a range of
one to twenty hours.

15. • Exponential growth
• The number of progeny virus produced within
the infected cell increases exponentially for a
period of time, then reaches a plateau, after
which no additional increase in virus yield
occurs.

16. • The maximum yield per cell is characteristic
for each virus-cell system, and reflects the
balance between the rate at which virus
components continue to be synthesized and
assembled into virions, and the rate at which
the cell loses the synthetic capacity and
structural integrity needed to produce new
virus particles. This may be from 8 to 72 hours
or longer, with yields of 100 to 10,000 virions
per cell.

17. • Steps in the Replication Cycles of Viruses
• The individual steps in the virus replication
cycle are presented below in sequence,
• virus attachment to the host cell
• leading to penetration
• uncoating of the viral genome.
• Gene expression and replication are followed
by assembly and release of viral progeny.

19. • Adsorption
• The initial attachment of a virus particle to a
host cell involves an interaction between
specific molecular structures on the virion
surface and receptor molecules in the host cell
membrane that recognize these viral
structures (Figure 23.8A).

20. • Attachment sites on the viral surface: Some
viruses have specialized attachment
structures, such as the glycoprotein spikes
found in viral envelopes (for example,
rhabdoviruses, see p. 310); whereas for
others, the unique folding of the capsid
proteins forms the attachment sites (for
example, picornaviruses, see p 284).

22. • In both cases, multiple copies of these
molecular attachment structures are
distributed around the surface of the virion.
[Note: In some cases, the mechanism by
which antibodies neutralize viral infectivity is
through antibody binding to the viral
structures that are required for adsorption
(Figure 23.8B).]

23. • Host cell receptor molecules:
The receptor molecules on the host cell
membrane are specific for each virus family. Not
surprisingly, these receptors have been found to
be molecular structures that usually carry out
normal cell functions.

24. For example, cellular membrane receptors for
compounds such as growth factors may also
inadvertently serve as receptors for a particular
virus. Many of the compounds that serve as
virus receptors are present only on specifically
differentiated cells or are unique for one animal
species.

25. • Therefore, the presence or absence of host
cell receptors is one important determinant of
tissue specificity within a susceptible host
species, and also for the susceptibility or
resistance of a species to a given virus.

26. • Penetration
• Penetration is the passage of the virion from
the surface of the cell, across the cell
membrane and into the cytoplasm.
• There are two principal mechanisms by which
viruses enter animal cells:
• receptor-mediated endocytosis
• direct membrane fusion.

28. • Receptor-mediated endocytosis: This is
basically the same process by which the cell
internalizes compounds such as growth
regulatory molecules and serum lipoproteins,
except the infecting virus particle is bound to
the host cell surface receptor in place of the
normal ligand (Figure 23.9).

29. • The cell membrane invaginates, enclosing the virion in
an endocytotic vesicle (endosome). Release of the
virion into the cytoplasm occurs by various routes,
depending on the virus but, in general, it is facilitated
by one or more viral molecules. In the case of an
enveloped virus, its membrane may fuse with the
membrane of the endosome, resulting in the release of
the nucleocapsid into the cytoplasm.

31. • Membrane fusion: Some enveloped viruses
(for example, human immunodeficiency virus,
see p. 297) enter a host cell by fusion of their
envelope with the plasma membrane of the
cell (Figure 23.10). One or more of the
glycoproteins in the envelope of these viruses
promotes the fusion.

33. • The end result of this process is that the
nucleocapsid is free in the cytoplasm, whereas
the viral membrane remains associated with
the plasma membrane of the host cell.

34. • Uncoating
• refers to the stepwise process of disassembly of
the virion that enables the expression of the viral
genes that carry out replication. For enveloped
viruses, the penetration process itself is the first
step in uncoating. In general, most steps of the
uncoating process occur within the cell and
depend on cellular enzymes; however in some of
the more complex viruses, newly synthesized viral
proteins are required to complete the process.

35. • The loss of one or more structural
components of the virion during uncoating
predictably leads to a loss of the ability of that
particle to infect other cells, which is the basis
for the eclipse period of the growth curve (see
Figure 23.7). It is during this phase in the
replication cycle that viral gene expression
begins.

36. • Mechanisms of DNA virus genome replication
• Each virus family differs in significant ways
from all others in terms of the details of the
macromolecular events comprising the
replication cycle. The wide range of viral
genome sizes gives rise to great differences in
the number of proteins for which the virus can
code.

37. • In general, the smaller the viral genome, the
more the virus must depend on the host cell
to provide the functions needed for viral
replication

38. • For example, some small DNA viruses, such as
polyomavirus (see p. 249), produce only one
or two replication-related gene products,
which function to divert host cell processes to
those of viral replication.

39. • Other larger DNA viruses, such as poxvirus
(see p. 270) provide virtually all enzymatic and
regulatory molecules needed for a complete
replication cycle. Figure 23.11 outlines the
essential features of gene expression and
replication of DNA viruses

41. • Mechanisms of RNA virus genome replication
• Viruses with RNA genomes must overcome
two specific problems that arise from the
need to replicate the viral genome, and to
produce a number of viral proteins in
eukaryotic host cells. First, there is no host cell
RNA polymerase that can use the viral
parental RNA as a template for synthesis of
complementary RNA strands.

42. • Second, translation of eukaryotic mRNAs
begins at only a single initiation site, and they
are, therefore, translated into only a single
polypeptide. However, RNA viruses, which
frequently contain only a single molecule of
RNA, must express the genetic information for
at least two proteins: an RNA-dependent RNA
polymerase and a minimum of one type of
capsid protein.

43. • Although the replication of each RNA virus
family has unique features, the mechanisms
evolved to surmount these restrictions can be
grouped into four broad patterns (or
“types―) of replication.

44. • Type I: RNA viruses with a single-stranded
genome (ssRNA) of (+) polarity that replicates
via a complementary (-) strand intermediate:
• In Type I viral replication, the infecting
parental RNA molecule serves both as mRNA
and later as a template for synthesis of the
complementary (-) strand (Figure 23.12).

46. • Role of (+) ssRNA as mRNA: Because the parental
RNA genome is of (+), or messenger, polarity, it can
be translated directly upon uncoating and associating
with cellular ribosomes.

47. • The product is usually a single polyprotein from
which individual polypeptides, such as RNA-
dependent RNA polymerase and various proteins of
the virion, are cleaved by a series of proteolytic
processing events carried out by a protease domain
of the polyprotein (see Figure 23.12).

48. • Role of (+) ssRNA as the template for
complementary (-) strand synthesis:
• The viral (+) ssRNA functions early in infection,
not only as mRNA for translation of
polyproteins but also as a template for virus-
encoded RNA-dependent RNA polymerase to
synthesize complementary (-) ssRNA (see
Figure 23.12).

49. • The progeny (-) strands, in turn, serve as
templates for synthesis of progeny (+) strands,
which can serve as additional mRNAs,
amplifying the capacity to produce virion
proteins for progeny virus.

50. • When a sufficient quantity of capsid proteins
has accumulated later in the infection,
progeny (+) ssRNAs begin to be assembled
into newly formed nucleocapsids.

51. • Type II: Viruses with a ssRNA genome of (-)
polarity that replicate via a complementary (+)
strand intermediate:
• Viral genomes with (-) polarity, such as the (+)
strand genomes, also have two functions:
• 1) to provide information for protein
synthesis, and
• 2) to serve as templates for replication.

52. • Unlike (+) strand genomes, however, the (-)
strand genomes cannot accomplish these
goals without prior construction of a
complementary (+) strand intermediate
(Figure 23.13).

54. • A) Mechanism of replication of viral ssRNA with (-)
polarity: The replication problems for these viruses
are two-fold. First, the (-) strand genome cannot be
translated and, therefore, the required viral RNA
polymerase cannot be synthesized immediately
following infection.

55. • Second, the host cell has no enzyme capable of
transcribing the (-) strand RNA genome into (+)
strand RNAs capable of being translated. The
solution to these problems is for the infecting virus
particle to contain viral RNA-dependent RNA
polymerase, and to bring this enzyme into the host
cell along with the viral genome.

56. • As a consequence, the first synthetic event after
infection is transcription of (+) strand mRNAs from
the parental viral (-) strand RNA template.

57. • B) Mechanisms for multiple viral protein synthesis in
Type II viruses: The synthesis of multiple proteins is
achieved in one of two ways among the (-) strand
virus families: 1) the viral genome may be a
polycistronic molecule, from which transcription
produces a number of mRNAs, each specifying a
single polypeptide;

58. • 2) alternatively, the (-) strand viral genome may be
segmented (that is, composed of a number of
different RNA molecules, most of which code for a
single polypeptide).

59. • Production of infectious virus particles: Although the
details differ, the flow of information in both
segmented and unsegmented genome viruses is
basically the same. In the Type II replication scheme,
an important control element is the shift from
synthesis of (+) strand mRNAs to production of
progeny (-) strand RNA molecules that can be
packaged in the virions.

60. • This shift is not a result of different polymerase, but
rather to the sequestering of (+) strand RNA
molecules by interaction with one or more of the
newly synthesized proteins. This makes the (+)
strands available as templates for the synthesis of
genomic (-) strands. Further, segmented genome
viruses have the additional problem of assuring that
all segments are incorporated into the progeny
virions. The mechanism by which this occurs is not
clear.

61. • Type III: Viruses with a dsRNA genome.
• The dsRNA genome is segmented, with each
segment coding for one polypeptide.
However, eukaryotic cells do not have an
enzyme capable of transcribing dsRNA.

63. • Type III viral mRNA transcripts are, therefore,
produced by virus-coded, RNA-dependent
RNA polymerase (transcriptase) located in a
subviral core particle. This particle consists of
the dsRNA genome and associated virion
proteins, including the transcriptase.

64. • The mechanism of replication of the dsRNA is
unique, in that the (+) RNA transcripts are not
only used for translation, but also as
templates for complementary (-) strand
synthesis, resulting in the formation of dsRNA
progeny.

65. • Type IV: Viruses with a genome of ssRNA of (+)
polarity that is replicated via a DNA
intermediate.
• The conversion of a (+) strand RNA to a
double-stranded DNA is accomplished by an
RNA-dependent DNA polymerase, commonly
referred to as a reverse transcriptase,•that is
contained in the virion.

66. • The resulting dsDNA becomes integrated into
the cell genome by the action of a viral
integrase.•Viral mRNAs and progeny (+) strand
RNA genomes are transcribed from this
integrated DNA by the host cell RNA
polymerase.

68. Assembly and release of progeny
viruses.
Assembly of nucleocapsids generally takes place
in the host cell compartment where the viral
nucleic acid replication occurs (that is, in the
cytoplasm for most RNA viruses and in the
nucleus for most DNA viruses).

69. • For DNA viruses, this requires that capsid
proteins be transported from their site of
synthesis (cytoplasm) to the nucleus. The
various capsid components begin to self-
assemble, eventually associating with the
nucleic acid to complete the nucleocapsid.

70. • Naked viruses:
• In naked (unenveloped) viruses, the virion is
complete at this point. Release of progeny is
usually a passive event resulting from the
disintegration of the dying cell and, therefore,
may be at a relatively late time after infection.

71. • Enveloped viruses:
In enveloped viruses, virus-specific glycoproteins
are synthesized and transported to the host cell
membrane in the same manner as cellular
membrane proteins.1 When inserted into the
membrane, they displace the cellular
glycoproteins, resulting in patches on the cell
surface that have viral antigenic specificity.

72. • The cytoplasmic domains of these proteins
associate specifically with one or more
additional viral proteins (matrix proteins) to
which the nucleocapsids bind. Final
maturation then involves envelopment of the
nucleocapsid by a process of budding (Figure
23.16).

73. • A consequence of this mechanism of viral
replication is that progeny virus are released
continuously while replication is proceeding
within the cell and ends when the cell loses its
ability to maintain the integrity of the plasma
membrane.

74. • A second consequence is that with most
enveloped viruses, all infectious progeny are
extracellular. The exceptions are those viruses
that acquire their envelopes by budding
through internal cell membranes, such as
those of the endoplasmic reticulum or
nucleus.

75. • Viruses containing lipid envelopes are
sensitive to damage by harsh environments
and, therefore, tend to be transmitted by the
respiratory, parenteral, and sexual routes.
Nonenveloped viruses are more stable to
hostile environmental conditions and often
transmitted by the fecal-oral route.

77. Effects of viral infection on the host
cell
• The response of a host cell to infection by a virus
ranges from:
• 1) little or no detectable effect;
• to 2) alteration of the antigenic specificity of the
cell surface due to presence of virus
glycoproteins;
• to 3) latent infections that, in some cases, cause
cell transformation; or, ultimately,
• to 4) cell death due to expression of viral genes
that shut off essential host cell functions (Figure
23.17).

78. • Viral infections in which no progeny virus are
produced: In this case, the infection is referred
to as abortive. An abortive response to
infection is commonly caused by: 1) a normal
virus infecting cells that are lacking in
enzymes, promoters, transcription factors, or
other compounds required for complete viral
replication, in which case the cells are referred
to as nonpermissive;

79. • 2) infection by a defective virus of a cell that
normally supports viral replication (that is, by
a virus that itself has genetically lost the
ability to replicate in that cell type);
• or 3) death of the cell as a consequence of the
infection, before viral replication has been
completed.

80. • Viral infections in which the host cell may be
altered antigenically but is not killed, although
progeny virus are released:
• In this case, the host cell is permissive, and
the infection is productive (progeny virus are
released from the cell), but viral replication
and release neither kills the host cell nor
interferes with its ability to multiply and carry
out differentiated functions.

81. • The infection is therefore said to be persistent.
The antigenic specificity of the cell surface
may be altered as a result of the insertion of
viral glycoproteins.

82. Viral infections that result in a latent
viral state in the host cell:
• Some viral infections result in the persistence
of the viral genome inside a host cell with no
production of progeny virus. Such latent
viruses can be reactivated months or years in
the future, leading to a productive infection.
Some latently infected cells contain viral
genomes that are stably integrated into a host
cell chromosome.

83. • This can cause alterations in the host cell
surface, cellular metabolic functions, and,
significantly, cell growth and replication
patterns. Such viruses may induce tumors in
animals; in this case, they are said to be tumor
viruses, and the cells they infect are
transformed.

84. • Viral infections resulting in host cell death and
production of progeny virus:
• Eliminating host cell competition for synthetic
enzymes and precursor molecules increases
the efficiency with which virus constituents
can be synthesized.

85. • Therefore, the typical result of a productive
(progeny-yielding) infection by a cytocidal
virus is the shut-off of much of the cell's
macromolecular syntheses by one or more of
the virus gene products, causing the death of
the cell. Such an infection is said to be lytic.
The mechanism of the shut-off varies among
the viral families.