Beginning with the researched phylogenies and theories behind the origins of the HIV virus. The consensus seems to point to a cross-speciation origin but there are still various theories that are still under investigation. Firstly, the microbiology aspects of the virus need to be discussed in order to understand the complexity of the HIV virus. Since the virus is a retrovirus it performs reverse transcriptase, which is necessary for the viruses replication cycle, this creates a DNA copy from the RNA genome; this DNA copy contains a long terminal repeat that is continually being inserted into each host cell invaded (Brown and Holmes, 1994). Because retroviruses do not contain any proofreading abilities, during the process of reverse transcriptase, this causes a great amount of mutations within the same strands of the virus, meaning the virus is rapidly mutating itself (Hutchinson, 2001). Therefore, when scientists attempt to pinpoint the single origin of the HIV virus there are multiple obstacles that hinder their ability to find conclusive results.
The obstacles do not stop researchers from coming close to a definite answer. Scientists have used molecular clocks, phylogenetic studies, and evolutionary biology to identify the origins of the HIV virus. Most research executed has been focused on cross-speciation; hence most of the research has been dating the simian immunodeficiency virus (SIV) and using phylogenetic studies to determine whether or not the HIV virus is closely or genetically similar to the SIV virus. In summary, the HIV-1 strain has been closely similar to four distinct monkeys affected by the SIV virus while the HIV-2 strain has been more closely related to the SIV virus that affected sooty mangabeys (Brown and Holmes, 1994). Additionally, the HIV-2 strain has been theorized to originate from Haiti and possibly spread through tourism sexual contact (Barrett et al., 1998); this theory can be explained through global distribution maps that show higher frequency in Haiti and North America while HIV-2 strains are more frequent in western and central Africa.
Other individuals are more interested in the time frame where the HIV virus emerged. Scientists have attempted to determine the exact time when the HIV virus emerged through molecular evolutionary investigations; this is accomplished through studying the HIV sequence divergence between nucleotide sequences (Brown and Holmes, 1994). Although the time frame seems to be unclear, scientists support the use of primate immunodeficiency trees to compare the distances between primate lentiviruses and the emergence of the HIV virus (Brown and Holmes, 1994). Another suggestion shows that immunodeficiency viruses have been impacting mammals even before the HIV virus emerged even as much as a million years ago, and that the viruses simply co-evolved depending on the available host (Brown and Holmes, 1994). This is a distinct theory and there is not as much research on this...