Origin of HIV1 and HIV2: cross-species transmission of SIV to humans.
The phylogenetic tree from your analysis shows two separate clusters. One
contains SIV from chimpanzee (SIVCZ) together with the HIV1 sequences, while
the other contains SIV from macaque/sooty mangabey together with HIV2. This
indicates that HIV1 originated from one event where a virus was transmitted
from (presumably) chimpanzees to humans, while HIV2 originates from a second,
independent event where virus was transmitted from (presumably) sooty
mangabey to humans. The fact that viruses as deadly as HIV can suddenly appear
as a result of cross-species transmission obviously has rather serious implications.
In fact, several theories have been proposed for the origins of the AIDS virus in the
human population; these have ranged from conspiracy theories, for example
involving germ warfare research in laboratories, to explanations involving the
contamination of vaccines with monkey virus. Early polio vaccines are known to
have been contaminated with at least one monkey virus, SV40, and it has been
proposed that a similar scenario could have occurred with HIV (Elswood and
Stricker 1994). Other theories proposed include the direct inoculation of
monkey blood in malaria studies (Gilks 1991), the use of monkey blood as an
aphrodisiac in sexual practices (Noireau 1987), or even voodoo ritualism
involving the use of sacrificial animal blood (Smallman-Raynor et al. 1992).
However, there is no need to invoke vaccination programs or unusual sexual
practices to account for the transmission of SIV to humans. In many West
African countries sooty mangabeys are hunted for food and kept as pets (Marx et
al. 1991). Thus, scratches and bites of humans by monkeys or the exposure to
monkey blood while preparing food is the most likely cause of transmission
across the species-barrier.