4.1 Taxonomy of Microorganisms in Aquatic Environments 87
- The names of virus orders, families, subfamilies,
genera, and species should be written in italics with
the first letter capitalized. - Other words are not capitalized unless they are
proper nouns, e.g., Tobacco mosaic virus, Poliovirus,
Murray River encephalitis virus. - This format should only be used when official taxo
nomic entities are referred to it is not possible to
centrifuge the species, for example, Poliovirus, but
it is possible to centrifuge poliovirus. - Italics and capitalization are not used for vernacular
forms (e.g., rhinoviruses, c.f. the genus Rhinovirus),
for acronyms (e.g., HIV1), nor for adjectival usage
(e.g., poliovirus polymerase).
4.1.7.2 The Viral Groups
DNA Viruses (Groups I and II)
Group I: These are doublestranded DNA viruses and
include such virus families as Herpesviridae (examples
like HSV1 [oral herpes], HSV2 [genital herpes], VZV
[chickenpox], EBV [Epstein–Barr virus], CMV
[Cytomegalovirus]), Poxviridae (smallpox), and many
tailed bacteriophages. The mimivirus is also placed
into this group (see Table 4.1 0 ).
Group II: These viruses possess singlestranded
DNA and include such virus families as Parvoviridae
and the important bacteriophage M13 (see
Table 4.1 1 ).
RNA Viruses (Groups III, IV and V)
Group III: These viruses possess doublestranded RNA
genomes, e.g., rotavirus. These genomes are always
segmented. Segmented virus genomes are those which
are divided into two or more physically separate
molecules of nucleic acid, all of which are then
packaged into a single virus particle (see Table 4.12).
Group IV: These viruses possess positivesense single
stranded RNA genomes. Many well known viruses are
found in this group, including the picornaviruses
(which is a family of viruses that includes wellknown
viruses like Hepatitis A virus, enteroviruses, rhinovi
ruses, poliovirus, and footandmouth virus), SARS
virus, hepatitis C virus, yellow fever virus, and rubella
virus. Positivesense viral RNA is identical to viral
mRNA and thus can be immediately translated by the
host cell (see Table 4.1 3 ).
Group V: These viruses possess negativesense single
stranded RNA genomes. The deadly Ebola and
Marburg viruses are well known members of this
group, along with influenza virus, measles, mumps,
and rabies. Negativesense viral RNA is complemen
tary to mRNA and thus must be converted to positive
sense RNA by an RNA polymerase before translation
(see Table 4.14).Reverse Transcribing Viruses (Groups VI and VII)
A reverse transcribing virus is any virus which
replicates using reverse transcription, the formation of
DNA from an RNA template. Both Group VI and
Group VII viruses fall into this category. Group VI
contains singlestranded RNA viruses which use a
DNA intermediate to replicate, whereas Group VII
contains doublestranded DNA viruses which use an
RNA intermediate during genome replication. Thus a
reverse transcriptase, also known as RNAdependent
DNA polymerase, is a DNA polymerase enzyme that
transcribes singlestranded RNA into singlestranded
DNA. Normal transcription involves the synthesis of
RNA from DNA; hence, reverse transcription is the
reverse of this.
Group VI: RNA Reverse Transcribing Viruses possess
singlestranded RNA genomes and replicate using
reverse transcriptase. The retroviruses are included in
this group, of which HIV is a member. Members of
Group VI use virally encoded reverse transcriptase, a
RNAdependent DNA polymerase, to produce DNA
from the initial virion RNA genome. This DNA is
often integrated into the host genome, as in the case of
retroviruses and pseudoviruses, where it is replicated
and transcribed by the host. Group VI includes the fol
lowing in Table 4.1 5.
Group VII: DNA Reverse Transcribing Viruses possess
doublestranded DNA genomes and replicate using
reverse transcriptase. The hepatitis B virus can be found
in this group. Group VII have DNA genomes contained
within the invading virus particles. The DNA genome is
transcribed into both mRNA, for use as a transcript in
protein synthesis, and pregenomic RNA, for use as the
template during genome replication. Virally encoded
reverse transcriptase uses the pregenomic RNA as a
template for the creation of genomic DNA. They are
shown in Table 4.1 6.The Structure of the DNA and RNA Viruses
The structures of the various viruses whether they are
DNA or RNA are highly variable. The structure of the
DNA viruses are shown in Table 4.1 7 and those of
the RNA viruses are shown in Table 4 .1 8.