Analysis of the Envelope Region of the Highly Divergent HIV-2 ALT Isolate Extends the Known Range of Variability Within the Primate Immunodeficiency Viruses

Abstract

HIV-2_ALT is a highly divergent HIV-2-related isolate that is genetically equidistant to the prototypic HIV-2 strains, defined by HIV-2_ROD, and to the simian immunodeficiency viruses SIV_mac and SIV_sm. We have now cloned and sequenced the envelope region of HIV-2_ALT, thus completing the analysis of the whole viral genome. The sequences of env and nef and of the second exons of tat and rev were compared with those of the other viruses of the HIV-2/SIV_sm/SIV_mac group. Despite of the high degree of variation of HIV-2_ALT, functional domains of the genes are conserved. Although in env, the overall pattern of constant and variable domains is maintained, many single amino acid exchanges exist at positions previously thought to be constant in HIV-2 strains. In addition, when compared with a broader spectrum of immunodeficiency viruses, which includes SIV_MND from mandrill and SIV_AGM from African green monkey, HIV-2_ALT Env has a high percentage of amino acid exchanges, which are unique to this strain. This underlines the separate branch of HIV-2_ALT within the phylogenetic tree and makes obvious the inclusion of such divergent strains in preventive and therapeutic programs.