VIRAL REPLICATION

General Steps in Viral Replication Cycles

A variety of different viral strategies have evolved for accomplishing multiplication
in parasitized host cells. Although the details vary from group to group, the general
outline of the replication cycles is similar. For a virus to replicate it must induce a
living host cell to synthesize all the essential components needed to make more
virions. These components must then be assembled into new virions that are released
from the cell. The viral replication cycle can be divided into five steps (Figure 1).
1. Attachment (adsorption) of the virion to a susceptible host cell: The first
step in viral infection is attachment, interaction of a virion with a specific
receptor site on the surface of a cell. Receptor molecules differ for different
viruses but are generally glycoproteins.

Figure 1: The replication cycle of a bacterial virus.

 2. Penetration (entry, injection) of the virion or its nucleic acid into the host
cell: After binding, the virus particle is taken up inside the cell. This step is
referred to as penetration or engulfment. In some systems, this is
accomplished by receptor-mediated endocytosis, with uptake of the ingested
virus particles within endosomes.

3. Synthesis of virus nucleic acid and protein by host cell metabolism as

redirected by the virus: The synthetic phase of the viral replicative cycle
ensues after uncoating of the viral genome. The essential theme in viral
replication is that specific mRNAs must be transcribed from the viral nucleic
acid for successful expression and duplication of genetic information. After
this is accomplished, viruses use cell components to translate the mRNA.

4. Assembly of capsids (and membrane components in enveloped viruses)

and packaging of viral genomes into new virions: This whole process is
called maturation. Newly synthesized viral genomes and capsid polypeptides
assemble together to form progeny viruses.

5. Release of mature virions from the cell: At the end of maturation, mature
virions are released, either as a result of cell lysis or by budding or excretion,
depending on the virus. The number of virions released, called the burst size,
varies with the particular virus and the particular host cell, and can range from
a few to a few thousand.

The Baltimore Classification Scheme and DNA Viruses

The virologist David Baltimore, who along with Howard Temin and Renato
Dulbecco shared the Nobel Prize for Physiology or Medicine in 1975 for the
discovery of retroviruses and reverse transcriptase, developed a classification
scheme for viruses. The Baltimore classification scheme (Table 1) is based on the
relationship of the viral genome to its mRNA and recognizes seven classes of
viruses.
Class Description of genome and replication strategy Examples
I Double-stranded DNA genome Herpesvirus, pox virus
II Single-stranded DNA genome Chicken anemia virus
III Double-stranded RNA genome Reoviruses
 IV Single-stranded RNA genome of plus configuration Poliovirus
V Single-stranded RNA genome of minus configuration Influenza virus, rabies
virus
VI Single-stranded RNA genome that replicates with DNA Retroviruses
intermediate
VII Double-stranded DNA genome that replicates with RNA Hepatitis B virus
intermediate

Figure 2a: Formation of mRNA and new genomes in DNA viruses.

 Double and Positive Strand DNA Viruses

Double-stranded (ds) DNA viruses are in class I. The mechanism of mRNA
production and genome replication of class I viruses is the same as that used by the
host cell genome, although different viruses use different strategies to ensure that
viral mRNA is expressed in preference to host mRNA.
Class II viruses are single-stranded (ss) DNA viruses. Before mRNA can be
produced from such viruses, a complementary DNA strand must be synthesized
because RNA polymerase uses double-stranded DNA as a template. These viruses
form a dsDNA intermediate during replication that is also used for transcription
(Figure 2a). The synthesis of the dsDNA intermediate and its subsequent
transcription can be carried out by cellular enzymes (although viral proteins may
also be required). The dsDNA intermediate is also used to generate the viral genome;
one strand becomes the genome while the other is discarded (Figure 2a). Until
recently, all known ssDNA viruses contained positive-strand DNA, which has the
same sequence as their mRNA (see positive-strand viruses below). However, a novel
virus is now known that contains circular ssDNA of negative polarity. Torque teno
virus (TTV), as this virus is called, is widespread in humans and other animals but
causes no obvious disease symptoms. The mode of replication of TTV has not yet
been fully investigated.

Figure 2b: Formation of mRNA and new genomes in RNA viruses. By convention, mRNA is
always considered to be of the plus (+) orientation.
 Positive- and Negative-Strand RNA Viruses
The production of mRNA and genome replication is different for RNA viruses
(classes III–VI). Recall that mRNA is complementary in base sequence to the
template strand of DNA. By convention in virology, mRNA is of the plus (+)
configuration. Its complement is thus of the minus (-) configuration. This convention
is used to describe the genome of a single-stranded virus, whether its genome
contains RNA or DNA (Figure 2b). For example, a virus that has a ssRNA genome
with the same orientation as its mRNA is a positive-strand RNA virus, while a virus
whose ssRNA genome is complementary to its mRNA is a negative-strand RNA
virus.
Cellular RNA polymerases do not normally catalyze the formation of RNA from an
RNA template, but instead require a DNA template. Therefore, RNA viruses,
whether positive, negative, or double-stranded, require a specific RNA-dependent
RNA polymerase. The simplest case is the positive-strand RNA viruses (class IV)
in which the viral genome is of the plus configuration and hence can function directly
as mRNA (Figure 2b). In addition to other required proteins, this mRNA encodes a
virus specific RNA-dependent RNA polymerase (also called RNA replicase). Once
synthesized, this polymerase first makes complementary minus strands of RNA and
then uses them as templates to make more plus strands. These plus strands can either
be translated as mRNA or packaged as the genome in newly synthesized virions
(Figure 2b).
For negative-strand RNA viruses (class V), the situation is more awkward. The
incoming RNA is the wrong polarity to serve as mRNA, and therefore mRNA must
be synthesized first. Because cells do not have an RNA polymerase capable of this,
these viruses must carry some of this enzyme in their virions, and the enzyme enters
the cell along with the genomic RNA. The complementary plus strand of RNA is
synthesized by this RNA-dependent RNA polymerase and is then used as mRNA.
This plus-strand mRNA is also used as a template to make more negative-strand
genomes (Figure 2b). The dsRNA viruses (class III) face a similar problem.
Although the virion does contain plus-strand RNA, this is part of the dsRNA genome
and cannot be released to act as mRNA. Consequently, the virions of dsRNA viruses
must also contain RNA-dependent RNA polymerases that transcribe the dsRNA
genome to produce plus-strand mRNA upon entry into the host cell.
 Retroviruses
The retroviruses are animal viruses that are responsible for causing certain kinds of
cancers and acquired immunodeficiency syndrome, AIDS. Retroviruses have
ssRNA in their virions but replicate through a dsDNA intermediate (class VI). The
process of copying the information found in RNA into DNA is called reverse
transcription, and thus these viruses require an enzyme called reverse transcriptase.
Although the incoming RNA of retroviruses is the plus strand, it is not used as
mRNA, and therefore these viruses must carry reverse transcriptase in their virions.
After infection, the virion ssRNA is converted to dsDNA via a hybrid RNA–DNA
intermediate. The dsDNA is then the template for mRNA synthesis by normal
cellular enzymes.
Finally, class VII viruses are those that have double-stranded DNA in their virions
but replicate through an RNA intermediate. These unusual viruses also use reverse
transcriptase. The strategy these viruses use to produce mRNA is the same as that of
class I viruses (Figure 2a), although their DNA replication is very unusual because,
as we will see later, the genome is only partially double-stranded.