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and details of the replication machinery used by each virus
CLASSIFICATION OF VIRUSES
are given in the chapters that describe individual viruses.
Second, viruses must encode proteins that are used in the
The Many Kinds of Viruses
assembly of progeny viruses. For simpler viruses, these
Three broad classes of viruses can be recognized, which
may consist of only one or a few structural proteins that
may have independent evolutionary origins. One class,
assemble with the genome to form the progeny virion. More
which includes the poxviruses and herpesviruses among
complicated viruses may encode scaffolding proteins that
many others, contains DNA as the genome, whether single
are required for assembly but are not present in the virion.
stranded or double stranded, and the DNA genome is rep-
In some cases, viral proteins required for assembly may
licated by direct DNA DNA copying. During infection,
have proteolytic activity. Assembly of viruses is described
the viral DNA is transcribed by cellular and/or viral RNA
in Chapter 2. Third, many (most?) viruses encode proteins
polymerases, depending on the virus, to produce mRNAs for
that interfere with defense mechanisms of the host. These
translation into viral proteins. The DNA genome is replicated
defenses include, for example, the immune response and the
by DNA polymerases that can be of viral or cellular origin.
interferon response of vertebrates, which are highly evolved
Replication of the genomes of most eukaryotic DNA viruses
and effective methods of controlling and eliminating virus
and assembly of progeny viruses occur in the nucleus, but
infection; and the DNA restriction system in bacteria, so use-
the poxviruses replicate in the cytoplasm.
ful in molecular biology and genetic engineering, that pre-
A second class of viruses contains RNA as their genome and
vents the introduction of foreign DNA. Vertebrate defenses
the RNA is replicated by direct RNA RNA copying. Some
against viruses, and the ways in which viruses counter these
RNA viruses, such as yellow fever virus (family Flaviviridae)
defenses, are described in Chapter 10.
and poliovirus (family Picornaviridae), have a genome that is
It is obvious that viruses that have larger genomes and
a messenger RNA, defined as plus-strand RNA. Other RNA
encode larger numbers of proteins, such as the herpesviruses
viruses, such as measles virus (family Paramyxoviridae) and
(family Herpesviridae), have more complex life cycles and
rabies virus (family Rhabdoviridae), have a genome that is
assemble more complex virions than viruses with small
anti-messenger sense, defined as minus strand. The arenavi-
genomes, such as poliovirus (family Picornaviridae). The
ruses (family Arenaviridae) and some of the genera belonging
smallest known nondefective viruses have genomes of about
to the family Bunyaviridae have a genome that has regions of
3 kb (1 kb = 1000 nucleotides in the case of single-stranded
both messenger and anti-messenger sense and are called ambi-
genomes or 1000 base pairs in the case of double-stranded
sense. The replication of these viruses follows a minus-sense
genomes). These small viruses may encode as few as three
strategy, however, and they are classified with the minus-sense
proteins (e.g., the bacteriophage MS2). At the other extreme,
viruses. Finally, some RNA viruses, for example, rotaviruses
the largest known RNA viruses, the coronaviruses (family
(family Reoviridae), have double-strand RNA genomes. In the
Coronaviridae), have genomes somewhat larger than 30 kb,
case of all RNA viruses, virus-encoded proteins are required
whereas the largest DNA viruses, poxviruses belonging to
to form a replicase to replicate the viral RNA, since cells do
the genera Entomopoxvirus A and C (family Poxviridae),
not possess (efficient) RNA RNA copying enzymes. In the
have genomes of up to 380 kb. These large DNA viruses
case of the minus-strand RNA viruses and double-strand RNA
encode hundreds of proteins and can finely regulate their
viruses, these RNA synthesizing enzymes also synthesize
life cycle. Further, as stated before, many or even most
mRNA and are packaged in the virion, because their genomes
viruses interfere with host defenses. In the smaller viruses
cannot function as messengers. Replication of the genome
this may involve only one or two proteins that interfere with
proceeds through RNA intermediates that are complementary
limited aspects of host defense, whereas the large viruses
to the genome in a process that follows the same rules as DNA
have the luxury of encoding more than a dozen proteins that
replication.
can finely regulate the host defense mechanisms. It is worth-
The third class of viruses encodes the enzyme reverse
while remembering that even the largest viral genomes are
transcriptase (RT), and these viruses have an RNA DNA
small compared to the size of the bacterial genome (2000 kb)
step in their life cycle. The genetic information encoded by
and miniscule compared to the size of the human genome
(2 106 kb).
these viruses thus alternates between being present in RNA
and being present in DNA. Retroviruses (e.g., HIV, fam-
There are other subcellular infectious agents that are even
ily Retroviridae) contain the RNA phase in the virion; they
"smaller" than viruses. These include satellite viruses, which
have a single-stranded RNA genome that is present in the
are dependent for their replication on other viruses; viroids,
virus particle in two copies. Thus, the replication of their
small (~300 nucleotide) RNAs that are not translated and
genome occurs through a DNA intermediate (RNA DNA
have no capsid; and prions, infectious agents whose iden-
RNA). The hepadnaviruses (e.g., hepatitis B virus, family
tity remains controversial, but which may consist only of
Hepadnaviridae) contain the DNA phase as their genome,
protein. These agents are covered in Chapter 9.
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