Environmental Microbiology of Aquatic and Waste Systems

86 4 Taxonomy, Physiology, and Ecology of Aquatic Microorganisms

been abandoned owing to the small sizes of viruses
and because the disease symptoms of different viruses
were sometimes similar (Anonymous 2005 ; Sander
2007 ). The current classification of viruses is credited
to David Baltimore, who won the Nobel Prize for his
discovery of retroviviruses and reverse transcriptase.
According to the Baltimore classification, viruses are
grouped into seven based on their nucleic acid (DNA
or RNA), strandedness (single­stranded or double
stranded), and method of replication. The groups are
numbered with Roman numerals thus:
Group I: double­stranded DNA viruses
Group II: single­stranded DNA viruses
Group III: double­stranded RNA viruses
Group IV: positive­sense single­stranded RNA viruses
Group V: negative­sense single­stranded RNA viruses
Group VI: reverse transcribing diploid single­stranded
RNA viruses
Group VII: reverse transcribing circular double­stranded
DNA viruses

Nomenclature of viruses: The nomenclature of viruses
is based on a set of rules set up by the International
Committee on the Taxonomy of Viruses (ICTV), which
since the 1960s has been arranging viruses in these
seven groups into taxonomic hierarchies.

The criteria for the taxonomic arrangements are:

1. Morphology
   (Helical, e.g., bacteriophage M13; icosohedral/poly­
   hedral/cubic, e.g., poliovirus, enveloped – may have
   poyhedral (e.g., herpes simplex) or helical (e.g.,
   influenza virus) capsids, complex, e.g., pox viruses)


2. Nucleic acid type,


3. Whether the virus is naked or enveloped


4. Mode of replication


5. Host organisms


6. The type of disease they cause

4.1.7.1 Viral Taxonomy and Nomenclature

Viral taxonomic nomenclature is modeled after that of

cellular organisms. However viruses suffer from the

absence of fossil record which will enable more phylo­

genetic relationships among the various groups.

Consequently, the highest level in the viral taxonomic

hierarchy is the order, thus:

Order (­virales)

Family (­viridae)

Subfamily (­virinae)

Genus (­virus)

Species (­virus)

Regarding nomenclature, the rules set up by the

ICTV are as follows (Van Regenmortel 1999 ):

Nucleocapsid

Reverse-transcriptase

Integrase

Capsid

Protease

MATURE

VIRION

IMMATURE

Matrix

gp120-gp41

 2010

Swiss Institute of Bioinformatics

Fig. 4.26 Structure of HIV 1 virus (Reproduced with permission
from the Swiss Institute of Bioinformatics [SIB]; Anonymous 2010 c)
Note that the HIV 1 virus has an envelope (matrix in the dia­
gram above). Not all viruses have envelopes; those which do not
are said to be naked (see text). The gp structures are glycoprotein.

(Retroviral) integrase is an enzyme produced by a retrovirus that

enables its genetic material to be integrated into the DNA of the

infected cell. Note also the reverse transcriptase (produced by

retroviruses such as HIV), a DNA polymerase enzyme that tran­

scribes single­stranded RNA into double­stranded DNA