Possible acquisition and molecular evolution of vpu genes inferred from comprehensive sequence analysis of human and simian immunodeficiency viruses

Vpu, an accessory protein of Human immunodeficiency virus 1 (HIV-1), plays a crucial role in viral particle production and release, contributing to HIV virulence and its associated pandemic. Despite its significance, the acquisition and evolution of the vpu gene remain poorly understood. In this study, we conducted a comprehensive computational analysis of approximately 38,000 sequences from Simian immunodeficiency viruses (SIV) and HIV. From these, we obtained 141 representative Vpu protein sequences, while preserving their diversity by removing redundant sequences. We then created a phylogenetic tree, which revealed that SIV and HIV strains can be classified into four major types based on the Vpu proteins they express: Vpu-type 1, the putative ancestral type, which includes SIVs from Dent’s mona monkey, mona monkey, and moustached guenon; Vpu-type 2, which includes SIVgor from gorillas and HIV-1 group O; Vpu-type 3, which includes SIVcpz from chimpanzees; and Vpu-type 4, which includes HIV-1 group M, HIV-1 pandemic strain (subtype 4a), and HIV-1 group N (subtype 4b). Vpu-types 1 and 2 show variations in vpu length, whereas Vpu-types 3 and 4 show less variability. Notably, the gene encoding Vpu-type 1 varies in the length of its overlap with the env gene. To clarify the evolutionary relationship between Vpu-type 1 SIVs and SIVs lacking Vpu, we constructed a phylogenetic tree based on the nucleotide sequence between the pol and env genes, using 401 sequences derived from HIV-1, HIV-2, and SIVs. Vpu-type 1 (SIVden and SIVmon), SIVasc (red-tailed monkey), and SIVsyk (Sykes’ monkeys) clustered closely on the phylogenetic tree. Considering the observed similarities between the vpu, vpr and env genes in SIVdeb and SIVsyk, we speculated that the vpu gene originated within the SIV genome. A phylogenetic tree constructed with 242 Vpu-type 4a sequences from the HIV pandemic strain and 135 sequences of circulating recombinant forms of HIV-1 revealed that the viral subtypes can be further classified into 18 distinct protein subtypes, surpassing the number of previously known subtypes. Collectively, our results suggest an evolutionary model for the vpu gene that sheds light on its origin and divergence, and their implications in the context of HIV-1 and SIV evolution.