From The Annual Review of Ecology and
Systematics
Volume 25,
1994
The human immunodeficiency viruses, HIV-I and HIV-2, are members of a group of closely related viruses found in a number of different African primate species. More distantly related lentiviruses are found in several different mammalian orders. All are associated with long-term infections, but the outcome of infection ranges from a complete absence of symptoms to a rapidly developing immunodeficiency and death. While HIV-2 is probably directly related to a virus that is responsible for an asymptomatic infection in the Sooty Mangabey, no obvious candidate for the progenitor of HIV-I has yet been found. Substantial genetic diversity is present in all immunodeficiency viruses, and phylogenetic analysis of HIV-1 sequences obtained from a wide range of geographic locations has revealed 5-7 groups of viral strains, all equally distant from each other. All groups have been found in Africa, but their distribution elsewhere reflects chance links between individuals at high risk of infection. In some areas large epidemics have spread through groups of such individuals to infect thousands within a few months, resulting in an increase in the global frequency of the particular strain responsible, without the occurrence of any significant diversification. In contrast, within infected patients, substantial diversity is developed over the period of the infection, especially in regions of the envelope gene which are targets for immune recognition (frequency-dependent selection). However, this diversity appears to be reduced at transmission (stabilizing selection). Analysis of these different evolutionary forces gives insights into the development of drug resistance and to potentially protective immune responses which are of practical value, while providing novel observations on molecular evolution in real time.
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There is a common tendency for those involved in studying genetic variation in HIV, particularly the genetic variation of an HIV population within an infected individual, to misrepresent this variation as defining new taxa of HIV called "quasi-species" of HIV. The techniques of phylogenetic analysis are employed in describing evolutionary relationships through the creation of multi-branched evolutionary trees. While all this might make nice pictures as fillers for such publications, it has, in my opinion, no biological meaning. A comparison of nucleotide sequences is a powerful tool in describing populations, but is essentially meaningless without supporting evidence, particularly when the overall DNA homology is high, approaching 90% or higher in the case of so-called HIV "quasi-species".
Groupings of populations based solely on genetic diversity does not define new taxonomic groups. An essential criterion in describing these genetic groups are never involved in the analysis: a demonstration that the genetic variants are biological distinct, i.e., there are different niches utilized by each of the putative new taxa such that selection pressure results in increased genomic divergence. Otherwise, what is described is simply intrapopulation genetic variation.
For two strains of HIV-1 ( MN vs BRU) there is 90% DNA homology; HIV-1(MN) vs SIVAGM155(from african green monkeys), 60% DNA homology; HIV-1(MN) vs HIV-2ST, 58% DNA homology; and HIV-2ST vs SIVAGM155, 60% DNA homology. Additionally, HIV-1 will infect and cause AIDS only in humans, while HIV-2 can infect and cause AIDS in humans, macaques, and baboons. SIVAGM can infect both african green monkeys and macaques, but will produce disease, interestingly, only in macaques Thus, both genomic divergence as well as the biology of the virus define its' taxonomic position.