A Novel Construction of Genome Space with Biological Geometry

Yu, Chenglong; Liang, Qian; Yin, Changchuan; He, Rong L.; Yau, Stephen S.-T.

In order to further illustrate the efficiency of our genome space, we then focus on the origins and evolution of human immunodeficiency virus (HIV). HIV is a lentivirus that can lead to acquired immune deficiency syndrome (AIDS), a condition in humans in which the immune system begins to fail, leading to life-threatening opportunistic infections. To develop the anti-HIV drugs and vaccines, the research into the origins and evolution of this virus has become very important. Rambaut et al. 25 reconstructed the phylogenetic tree of the primate lentiviruses including HIV-1, HIV-2, and the simian immunodeficiency viruses (SIVs). It was discovered that the two human viruses are related to different SIVs and therefore have different evolutionary origins. However, in Rambaut et al.'s paper, the tree was constructed using the maximum likelihood method on an alignment of the nucleotide sequences of polymerase gene in these lentiviruses. Generally, a single-gene sequence does not possess enough information to construct an evolutionary history of organisms, thus we use our new method to reconstruct the phylogenetic tree based on the whole genome sequences.